I haven't heard other users having problems with files not being read from the server. Is this with a specific server or is it a problem you have with multiple servers? You can do some debugging yourself with the ftp, open the console in Wappler (bottom panel) and check the bug icon. It will then output all ftp information to the console.
If you can't figure out yourself, then post a bug report with a debug log.
I checked the exclude pattern, there seems to be some cases that it ignores the pattern. This seems to happen when for example a php file is saved and the target is set to the remote host. It then uploads the file even when it is in the ignore pattern. If there are other cases that you know where the pattern is ignored then please let us know.