Ok,
You have an ACOM member tree which is linked and syncs with the same named tree in the FTMM program, correct?
Do you auto or manually sync? I highly recommend using manual sync only. The sync function/settings are controlled from the FTMM program.
You have duplicate profiles of some individuals in the tree, correct? Do these same dupes present in both your ACOM member tree and the FTMM tree?
You are working on the tree from the ACOM site, correct? Is this routine, or do you sometimes work on-line from the FTMM program?
A record collection "search" cannot create a profile, however the results of a search, a census record for instance, which you are saving to one profile, can (by your choice) create profiles for other immediate family listed in the census transcription. Is it the during the "save" process the duplicates are being created?
This type of duplication is usually user-created and it's best avoided by manually (keying in the initial data for every profile in your tree) creating profiles, and then attaching the citations.
Before cleaning up the duplicates, and you'll be doing this from your ACOM member tree (ACOM website), open FTMM, turn of auto-sync, log-off of your ACOM account in the FTMM program and quit FTMM.
From the ACOM member tree program, use the merge profile function (found in every profile).. Keep a second tab open to the "List of all people", this is the easiest way to see which profiles are duplicated. This needs to be refreshed every time you make a change to the tree in another tab.
When you've successfully cleaned the member tree on ACOM, fire up FTMM, log on to ACOM and perform a sync.