There is the possibility that SSRs are not stable, but finding 2 out of 76 seems a very high occurrence, which is unlikely. Most likely is that you did have some cross pollination on your F1 plants in getting your F2. If so, these alleles will occur at non-mendelian frequencies in your F2.

Slipped-strand mispairing and subsequent errors in F1 during DNA replication , repair or recombination can lead to occurrence of non parental alleles in F2

I think this may be out crossing