While the stats that DK has come up with certainly point to something, I'm probably with Morgs as to the cause. I'm inherently sceptical of conspiracy theories in general, and so my tendency is to blame something like this on more typical human traits such as incompetence. A couple of problems to note are:
i. In any set of stats there is going to be a range - if there are an average number of frees for and against, then there are going to be variations - these are what produce the average. In that sense, I tend to think that certain team styles will tend to produce more or less free kicks, and that we therefore seem to have a style that sees us more likely to have kicks paid against us more often.
ii. Basically, we are much more forensic in our analysis of Fremantle than any other team. Having gone over a couple of quarters or a couple of games to identify frees that should have been paid and frees that shouldn't, logically we would need to scrutinise every other game to the same level of detail to see if what happens in Freo games happens elsewhere at all - and this would need to be done over every round.
iii. In any other circumstance, we would suggest that if the person conducting the study is a supporter, they may have some bias. I know for myself, if there is a game where I start to support one of the teams, I find myself noticing 'missed' or incorrect frees than in a game where I'm neutral. This is not to say that you're wrong DK, just that it may simply be a pattern whose cause can never be explicitly identified, which isn't to say that this cause does not exist.