My boyfriend was helping a friend clean some land. Someone called the law and they were arrested for criminal trespassing and theft by taking. The land owner called the sheriffs office to make sure they weren't charging them for being on his land. They said we its OK because we are still going to charge him for violation of probation. Can they do this if he has not committed a crime?

The PO can, but the judge should dismiss any violation once they get to court.
The police do not charge him with a probation violation, only his PO can do that.