You're right. I assume that it has to do something with SD2Vita itself. Someone on r/vita posted a thread the same error,
someone commented a solution for it, and it was really mentioned a lot on 6-7 years old threads. If you're still having the issue it's worth a try...
I've yet to try YAMT with SD2VITA but I tried it with an USB flash drive on the PS TV and I had
this problem, which is a different one.
@Anderxale said the PS TV sometimes won't start the USB drive immediately and it doesn't get mounted. If the PS TV is started this way, it will show the bubbles that it has installed only on the drive that booted (maybe internal storage or a Memory Card) and everything else will disappear. Restarting the PS TV is usually enough to reconnect the drive and the latter may be removed and reinserted before turning on the console to help. Apps and games will supposedly be back to LiveArea after restarting the PS TV, but like I
said, I still had that issue sometimes after doing it multiple times, and even if I didn't, I wanted a permanent solution, since I didn't want to restart the console every time I had
that problem (and that didn't even always work). Anyway, this no longer matters because I stopped using an USB flash drive on the PS TV but SD2VITA so even if for some reason I use YAMT in the future again, I'll use it with SD2VITA as well.
I won't try YAMT again in both the PS Vita and PS TV (and I won't use an USB flash drive on the PS TV again, even if using StorageMgr) since StorageMgr is working fine, I might have
said problem and I'm tired of having issues and reinstalling things in both consoles.
EDIT: Apparently,
said problem is
known and it really happens only on some microSD cards. On wakeup, the SD driver checks some fields that aren't present on all SD cards. Alternative YAMT mode is planned but nothing concrete yet.
EDIT 2: It seems the information regarding Samsung microSD cards was removed from
this website and it also says to use StorageMgr if using an USB drive and not YAMT so maybe
said problem is known.