When I run a nette app, I see an error on a line of code that doesn't exist anymore. Actually, I have changed that line of code but Tracy shows the code before changing it.
I tried removing temp/cache folder but it didn't fix the issue.
I'm running the app on my local machine using php -S localhost:8000 -t www command.
temp/cache is only directory Nette uses for generated files and in debug mode generated DIC from nette/bootstrap and generated templates from nette/latte should always be reloaded on change. If removing that directory did not help, it's probably not Nette-related.
Ensure you actually saved the file and if you run the code on remote machine that it also uploaded successfully.
Also check your OPcache settings and Cache-Control and Pragma headers, content may be cached too aggresively.