That's not a uniquely Thailand thing. Any country can have thieving bank employees. But there's no grand conspiracy for banks to steal from customers in Thailand.
Visa exempt is legitimate. But tourists are not meant to stay in Thailand long-term. They are warned the same as people with visa exempt. Tourist entry is tourist entry.
So she co-signed for a loan, and then the person who was supposed to pay didn't, and they took it from her account? Doesn't exactly seem like theft. Seems like she's not good at decision making.
You can ignore anything these bank managers say. They will say whatever they can to get you out of their business. I literally just read a report that someone got their bank letter from Bangkok Bank for monthly transfers YESTERDAY. As I said, if your bank branch will not help, go to a different one. They're a bunch of liars. The sooner you can be done with them, the better.
Regarding how the transfer shows, you need to see what bank it came from, and then go to that bank and ask them for a credit advice showing the transfer was international. Bring that along with your own bank account information for confirmation to immigration.
As far as the bank letter goes, this is far from the first report that they are refusing to issue the letter for monthly transfers. Most reports I've seen about this indicated the person went to a different branch and got the letter there without issue.
My advice is to switch to Kasikorn or another bank as soon as possible. Drop the garbage Bangkok Bank.
There is no rule that states xx number of days is or is not allowed in a year as a tourist.
That being said, immigration does not look kindly on people trying to stay long-term in Thailand without a long-term visa. The calendar year has nothing to do with it. You will not get away with doing 180 days ending in December only to return for 180 days in January.