anoop_pulakanti Seeing that behavior as well, but that was also present with v2 (except the temp folder name was tmp*, now it's tmpEXO*)... In multithreaded scenario's calling Disconnect-ExchangeOnline sometimes affected other threads (which seems to be solved in the v3 REST version), so it was actually a lot worse. I'm assuming there's a lock on the folder when Disconnect-ExchangeOnline tries to delete it (e.g. anti-X still scanning the folder), so it doesn't get cleaned up properly.
Best thing to do is to add some cleanup of the temp folders after calling Disconnect-ExchangeOnline, either depending on creation time (older than X), or (if you need a more aggressive approach) on folder contents (i.e. all folders without a psd1 in them can be safely removed).
Also, be aware that temp modules can be either created in the user's Temp folder ($ENV:TEMP) or the system temp folder (usually C:\Windows\Temp), so best to check both locations.