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Despite the popularity of Claude Code, Cursor, GitHub Copilot, and OpenAI Codex, developers have plenty of complaints about AI coding tools.
So researchers affiliated with York University and the University of Calgary in Canada decided to sift through developers' concerns about LLM-based integrated development environments (LIDEs) by analyzing Reddit discussions for common themes.
Their findings suggest that the builders of such tools failed to prioritize security and privacy, leaving developers to defend themselves.
Gias Uddin, associate professor at York University and a co-author of the research, told The Register that these tools are still relatively new and are evolving rapidly, which creates pressure to add new capabilities.
"Our study cannot say whether that pressure caused any particular problem, but it does show that many reported issues come from how these tools are designed and what access they are given, not simply from the underlying models," Uddin said. "In that sense, we believe prevention is better than cure; that is, security and privacy mechanisms should be built into the design before a tool is given broad access to a developer’s files, data, or systems."
Uddin and co-authors Mostafijur Rahman Akhond, Md Afif Al Mamun, and Song Wang say they wanted to look beyond the known issues with AI-generated code at LLM-based tooling and how developers interact with it.
They describe their findings in a preprint paper titled "'Impossible to hide secret …': Uncovering Security and Privacy Issues in LLM-native IDEs," accepted at the 41st IEEE/ACM International Conference on Automated Software Engineering (ASE), 2026.
Starting from a set of 1.1 million Reddit posts, they identified 446 posts and more than 6,000 comments to develop a taxonomy of security and privacy issues associated with using these LIDEs for AI-assisted coding.
"Our taxonomy reveals a broad range of developer-reported concerns, including unauthorized file operations, unsafe or unexpected code execution, triggering of destructive actions, opaque data flows, telemetry collection, and potential leakage of sensitive information through expanded context access," the authors state.
Some 43.1 percent of the posts covering security-related issues involved unauthorized file operations.
These involved LIDEs removing project directories or files without authorization (28.3 percent). Users also described AI tooling modifying files without explicit user consent (8.8 percent), as well as accessing content beyond the active workspace (5.7 percent).
"In one severe case (1npqf2f), Claude Code executed chmod +x on scripts without consent (File Permission Changes 0.6%)," the paper recounts. "Although rare, such actions pose disproportionate security risks."
Another set of posts describes operational safety issues arising from LIDE use, including impacts on production services. These accounted for 23.9 percent of security-related posts. Examples cited include reports of Replit removing a SaaS production database and Cursor deploying code to production despite an explicit directive not to do so.
A third category of woes covers unsafe code generation (18.2 percent). This involves incidents like nine VirusTotal detections reported for Cursor-generated software and hallucination-driven code changes: "When using Cursor, I noticed that after more than 10 rounds of dialogue, it starts to hallucinate and secretly modify code outside the requirements…"
Then there are the instances where these LIDEs ignored user instructions, allow lists, gates, permission settings, or .ignore files, which account for 16.5 percent of the security-related posts, as well as third-party tool integration risks (4.7 percent).
As for privacy problems, these were mentioned in 194 posts and cover issues like lack of transparency (45.9 percent) – the absence of clear information about what data an LIDE collects, retains, transmits, uses for training, or exposes to administrators – and unauthorized data access (23.7 percent).
Other privacy categories include privacy leakage violations (15.5 percent), unauthorized data collection and transmission (11.9 percent), and context integrity failures (8.8 percent), which refer to situations where "for example, a user of Claude Desktop reported receiving messages originating from another user’s session."
Uddin said, "We don’t think developers are completely unaware of these issues, as we found ongoing discussions about security and privacy concerns across many of these tools. Still, people continue to adopt them because they can make development faster and easier. They are also making programming more accessible to a wider group of people, including those with little formal programming experience or limited knowledge of software security."
Uddin said users cannot be expected to thoroughly understand which permissions are risky, which files need to be protected, or whether a tool is doing something it shouldn't.
"That makes it even more important for tool makers to build security into the tools themselves, with safer defaults and safeguards that do not depend on the user being a security expert," he said.
Even so, users of LIDEs are trying to manage the risks. The authors enumerate 13 mitigation strategies that developers have employed to get by. These fall into five general approaches: configuration management (33 percent); code governance (31 percent); data protection and privacy control (13 percent); isolation (13 percent); and external guidance (9 percent).
Based on their findings, the authors offer six recommendations. They advise: directing LIDE makers to implement proper security and privacy controls; enforcing security and privacy guardrails at an architectural level; incorporating a verification layer in LIDEs to validate generated code against security and privacy standards; establishing a formal protocol for assessing the trustworthiness of third-party tools; integrating sensitive file protection; and implementing strict security as a default.
"We believe secure defaults would be one of the most important improvements these tools could make," said Uddin. "Developers should not have to discover after something goes wrong that a tool had more access or freedom than they expected.
"Our findings point to practical measures such as limiting access to sensitive files by default, requiring clear approval before consequential actions, isolating projects and conversations, and making it easier to see and review what the tool is doing.
"Users should still have flexibility, but the safer option should be the starting point rather than something they have to configure themselves. In fact, developers from the Reddit posts in our study were already using many of these safeguards in ad hoc ways; we think several of them should be built into the tools and enabled by default." ®
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