To interpret this, we need to understand the terms used:-
1) OTAFM
=> Over The Air Folder Management
2) Entry not found in index
=> a typical Notes API call error when looking up a view and cannot find a document based on a key-value
3) folder reference is not found
=> this means that the key i.e. folder reference (probably a Ref ID) cannot be found
Since we're talking about Folder Management, it involves messages in a folder. My guess is that either:-
1) mail items were removed from user's state db due to state db pruning
2) mail items without any Ref ID (sometimes we see empty entries in the state db under mail items)
3) or like what Ajay has suggested - corrupted state db
If the user is not complaining, I will ignore this logging and leave the housekeeping taskk to the state db pruning job of the BES