In case you didn't know, it's possible to break down other Aura Break Zygarde you received from trades into cells, hence why it's possible to have more cells than what you found.
Let me explain how this works:
(1) Indicates whether the cell at that specific location has been collected.
(2) Shows how many of (1) + cores has been collected. In reality the game doesn't count the number of (1)'s collected; they just increase the counter by 1 whenever one is collected in-game. As a result, if not done correctly, there can be a mismatch between (1) and (2)
(3) This counts how many Cells you have left in your cube. Ones that you used to form a Zygarde is deducted from here, and ones you receive from breaking down a Zygarde gets added to here.
Sounds like you are talking about ORAS PKHeX editing bag bug.
Wait for an update. This has been reported multiple times already.