there are known issues with iCloud sync, see iCloud sync issues
- you could switch to the Obsidian sync (paid option)
- some users report success using the PC iCloud version for windows 7, 8
- personally I’m still doing manual cleanups of the extra …(1).md or …2.md files including those in the hidden .obsidian folder. Sometimes I have to kill the iCloud task and restart iCloud, sometimes I have to delete a file from iCloud.com so I can rename a …2.md back. It’s a bit of a hassle but with the file recovery option and backing up my files to dropbox I haven’t lost any data