Yes, I confirm that this problem has recently started happening in some markets. They can be changed to "finished" without any particular reason and then resumed, if a BetFair operator decides to delete a market and re-create it from a scratch, due to some mistake in the original market description.
Also, on some occasions, the exchange may not return a response to MF Pro's attempt to refresh a market, and in that case MF Pro thinks the market is finished.
We can tackle the latter (with the forthcoming update), but not the former I'm afraid.
I will announce the update in the Announcement section of the forum, but you can try the beta right now by downloading it from here:
MF Pro v. 8.8.1.3