Some monsters with either extremely low CRS (example: PF mite CR of 1/4) or extremely high (PF tarrasque with CR of 25) seem to have their CRs listed as 1/2. I also tried this with several creatures in 3.5, and the low CR creatures I tried (example human skeleton, rat) seem to have their CRs listed at 1/2. However, this is not true for the epic CR monsters (example: gibbering orb) in 3.5.
This seems to be two issues, actually. The tarrasque's CR is off because he has no CR entry in his races file listing. That assigns a default value of 0 to his CR, which is the internal representation of CR 1/2. The mite, however, does have a CR:1/4 entry in his races file listing, but still comes out as CR 1/2. I will have to explore this.
It might be helpful, to have PCGen report a warning for races that do not have a CR entry (unless the race has 0 racial hit dice, in which case the CR is determined by class levels alone).
This is actually a design flaw in the CR overhaul implementation. I'm working on a fix.
Fixed as of Subversion revision 25450.
Please back port this.