I'm glad to hear you solve the problem, if you have any issue about SharePoint, you are welcome to raise a ticket in this forum.
By the way, since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others.". So, I would make a brief summary of this thread:
[Currency column migrated without decimal separator with SPMT]
Issue Symptom:
OP need to migrate a SharePoint list from SP2016 on Prem to SP online. The list has several currency columns. Records that have currency with ,00 after the decimal like separator € 1000,00 are migrated correctly. Currency that has numbers behind the decimal separator like € 1000,99 are migrated wrong. e.g.:
€ 1000,00 in the source list is € 1000,00 in the destination list. € 1000,99 in the source list is € 100099,00 in the destination list.
Current status:
In Europe that's a point for thousand and a comma for decimals. So, OP checked 2016 server and there it was different from client where I run SPMT. OP changed those formatting settings on client, so they were the same as on the server and then the migration was performed correctly. So, turns out all locale and formatting settings need to be the same on the source server and the client you run SPMT on.
You could click the "Accept Answer" button for this summary to close this thread, and this can make it easier for other community member's to see the useful information when reading this thread. Thanks for your understanding!