The police charged both allegedly known characters, probably realizing that the stories each one were giving them were probably minimally related to the true facts, and decided to leave everything up to defense attorneys, prosecutors, judges, and juries to sort out. Police just are not paid enough, nor are there enough of them, nor is it even in their pay grade, to sort out scenarios like this. The absolute worst thing they could do is to 'assume the facts not in evidence' and make their charges based on these 'assumed facts', and missing the true crime. They charged him with 'break and enter' simply because some of the evidence available could imply that a 'break and enter' did happen, but it does not mean there actually was a 'break and enter' until a judge determines there was.

It is very common for police to lay charges that seem to fit the available evidence, but withdraw the charges when more evidence becomes available.

If I have a screwdriver in my hand, during some altercation, even if there was a legitimate reason for having it, I could be charged with having a dangerous weapon. The act of possessing the screwdriver itself itself says nothing about 'intent to harm', it is how that screwdriver was handled and used that determines the charge. In this case, that 'intent' could easily just have been inferred by hearsay evidence, and would not stand up in court.