This might be the case but it really isn’t the issue.I think I know what OP has done to raise suspicion (the circumstances seem to be specific to about 2/3 journeys within Greater Manchester), and it's made me curious.
I suspect I have the same 'home' station as OP: there are 'AP Northern Only' fares for about £3 less than a single to Manchester. I'll leave the rest to interpretation.
Notably the faresetter for the Any Permitted tickets for these journeys would be set by Transport for Greater Manchester. (potentially OPs case has nothing to do with TPE and that information is a red herring).
In my case, AP Northern Only is only valid on one of the 4tph to Manchester, the other three are run by TPE so I won't always buy the cheaper one if I don't want to wait around.
Would inconsistently buying different priced tickets for the same route be enough to show up on Northern's radar, even if I'd done nothing wrong?
Purchasing tickets is not illegal, using an invalid ticket is illegal. If Northern wish to secure a conviction then they have to prove to the court that the tickets were used illegally by the accused.