Prism 5.02 (Windows) and 5.0b (Mac) included a fix to a trivial bug in Fisher's exact test (when the two groups are identical, the P value should be 1.00 but earlier versions of Prism sometimes reported P values slightly greater than 1.0). Unfortunately, that fix introduced a new bug that occurs only when:

• You are using Prism 5.02 (Windows) or 5.0b (Mac). Earlier versions did not have this bug. Neither does InStat 3.0 or 3.1. 
• You have entered a symmetrical contingency table. A table is symmetrical when either the two row totals are identical, or the two column totals are identical. 
• You have chosen a two-tail (two-sided) P value. One-tail P values are computed correctly. 

The result of the bug is that the P value will be too low in some, but not all cases. In many cases, the discrepancy is tiny and won't affect your conclusions. In other cases, the discrepancy is larger and may affect your conclusion.

Of course, we will fix the bug in the next release of Prism: 5.03 and 5.0c.

It is easy to determine whether you have encountered this bug, and to compute the correct two-tail P value. With symmetrical contingency tables, the two-tail P value is exactly twice the one-tail P value (that is not always true with contingency tables that are not symmetrical). Therefore, to bypass the bug, ask Prism to compute a one-tail (one-sided) P value. This is a choice in the Parameters dialog for analyzing contingency table. To compute a two-tail P value, simply double the one-tail P value. 

More details and example.