The missing toe on the dead guy's body is on his right foot. When the bloody footprints appear at the station house, after Jim's ring is stolen, it's still the right foot that's missing the middle toe. But when Jim points out the footprints to Melinda, as he says 'the missing toe is on the right foot', he's pointing at a print made by the LEFT foot, which is now clearly missing the middle toe; the right foot now has all 5 toes showing in the print.
When Jim and the mortician discuss Bryan's corpse, the mortician first says that the body is a John Doe. Then when Jim asks about the missing toe, the mortician says that there is no mention of any surgery in his records. As a John Doe, he'd not have any records.
Alyssa's upcoming 10-year high school reunion is scheduled for February 24th, however this date has already passed since three episodes prior had a significant event happen on February 19th and more than five days have passed since that episode.