[Bug] Claude Code ignores user instructions and reprocesses already-handled files despite explicit guidance

Bug Description
it doesn't follow instructions. It makes decisions about processes that cost money (like APIs) and it keeps doing this even in the same session. It seems lazy and does the minimum path of effort. It needed to process 10 stories but there were 12 in the folder. Ir ran --dir so it reprocessed the two stories that didnt need to be processed even though before it did that I asked it to list the 10 stories to be processed. This has been an error-full session since the start

Environment Info

• Platform: win32
• Terminal: windows-terminal
• Version: 2.1.17
• Feedback ID: 1dfdfc5f-3a9a-44e1-9ada-63e749f63e2a

Errors

[{"error":"Error: ENOENT: no such file or directory, scandir 'C:\\ProgramData\\ClaudeCode\\.claude\\skills'\n    at readdirSync (unknown)\n    at <anonymous> (B:/~BUN/root/claude.exe:12:1903)\n    at kX (B:/~BUN/root/claude.exe:11:35097)\n    at readdirSync (B:/~BUN/root/claude.exe:12:1864)\n    at wF$ (B:/~BUN/root/claude.exe:1477:380)\n    at wF$ (B:/~BUN/root/claude.exe:1477:1350)\n    at <anonymous> (B:/~BUN/root/claude.exe:1477:4440)\n    at <anonymous> (B:/~BUN/root/claude.exe:1477:5171)\n    at A (B:/~BUN/root/claude.exe:11:7244)\n    at c7E (B:/~BUN/root/claude.exe:4782:4342)","timestamp":"2026-02-13T19:05:54.327Z"},{"error":"Error: ENOENT: no such file or directory, scandir 'C:\\Users\\guzta\\.claude\\skills'\n    at readdirSync (unknown)\n    at <anonymous> (B:/~BUN/root/claude.exe:12:1903)\n    at kX (B:/~BUN/root/claude.exe:11:35097)\n    at readdirSync (B:/~BUN/root/claude.exe:12:1864)\n    at wF$ (B:/~BUN/root/claude.exe:1477:380)\n    at wF$ (B:/~BUN/root/claude.exe:1477:1350)\n    at <anonymous> (B:/~BUN/root/claude.exe:1477:4483)\n    at <anonymous> (B:/~BUN/root/claude.exe:1477:5171)\n    at A (B:/~BUN/root/claude.exe:11:7244)\n    at c7E (B:/~BUN/root/claude.exe:4782:4342)","timestamp":"2026-02-13T19:05:54.327Z"},{"error":"Error: Request was aborted.\n    at makeRequest (B:/~BUN/root/claude.exe:160:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-14T00:32:13.121Z"},{"error":"Error: Request was aborted.\n    at makeRequest (B:/~BUN/root/claude.exe:160:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-14T00:32:15.997Z"}]