Erel,
When running B4A in an emulator, like Parallels Desktop on Mac, and storing files in a directory which is actually on the Mac filesystem (fairly standard procedure for Parallels Desktop - rather than storing user files within Windows on a Virtual Disk inside the VM) the Mac operating systme adds it's own hidden system files like DS_Store into the directory where the project is stored.
The B4A IDE then sees these hidden files and gives this warning:
You might want to code B4A to ignore Mac System files if they get added to a directory that holds a B4A project.
My project files are in the Mac filesystem (which Parallels maps to a Windows 7 User Files space so Windows thinks its saving to C:\Users\somename\ sub tree) so that files can be sync'd by dropbox (running on the Mac - not in the Windows VM).
Hope this helps,
Tim.