In the first "plot hole" I'm going to guess that Mas followed Nick at some point after his refusal to help him (which isn't hard to believe considering he wouldn't want him to get into any serious trouble).
As for the second one, you see an underling bring the second plate over to the table with the Oyabun shortly before the shootout takes place.
Lastly, the last scene with Nick giving Mas the plates was not meant to be seen as Mas suddenly turning into a bad cop. It was obviously Nick having a change of heart. He was probably planning on stealing the plates (or maybe he intended to give them back the whole time and was just having a laugh) and decided at the last minute to give them back to Mas after Mas mentioned the plates not being found. Mas is happy that Nick returned them as he suspected him to have taken them from his body language and tone of voice when he was asking him about them. He obviously feels bad about insinuating that Nick had taken them, ergo, he hits himself on the forehead with the cover of the box as a sort of self-punishment. He is going to return the plates as evidence, he's not going to use them to counterfeit money.
A bit long-winded, but that's my take on it.
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