This feature is key to my usage and I've not had this happen. Are you changing identifying tags (title / display artist / album) in between the play and the sync for these few songs? If they no longer match, MB will not be able to tell what it was supposed to be.
You can kind of see what MB has gotten from last.fm in the cache file. It's not plain text and not editable, but you can make it out for the most part in a text editor to at least see what's been received. It's usually at C:\Users\<Your User Name>\AppData\Local\MusicBee\InternalCache\LastFmPlayCountCache.dat
All these scrobbles are coming from my phone. I mostly listen to my music on the go and use MusicBee to organize my music collection, create playlists, and sync it all with my phone. As far as I know I have not changed tags for any of these songs, and they all occur in a row, so I don't think this is the issue. I looked over that cache file and the songs in question weren't in there (at least not toward the bottom with the other recent syncs).
I've noticed that I did play some songs through MusicBee on my laptop immediately before the ones I played on my phone that aren't Syncing with MusicBee:
Last scrobble from phone: 9/2 1:55 PM
3 songs scrobbled from MusicBee: 9/2 3:13 PM to 4:19 PM
Scrobbles from phone not syncing with MusicBee: 9/3 12:58 AM to 9/4 2:38 PM
Next song successfully synced from Last.FM to MusicBee: 9/4 2:42 PM
I'm not sure when I performed my next sync and noticed the issue, but there was no change in my phone or files in the period where the syncing succeeds again.