The number/identities of walkers and dead on the bus doesn't add up to the amount and who was seen in it leaving.
When Tara is talking to Glenn about the attack on the prison, it sounds like she says "I saw my sister and nephew", which makes no sense as the show only showed her sister and her niece.
However, this is because this isn't what she says; the subtitles make it clear she actually says "I saw my sister in that field."
When Glenn is first seen in a "long shot" there are chairs covering the door and his exit. However, when he goes to leave the chairs have been helpfully removed by one of the crew.
As Glenn collapses late in the episode, Tara yells his name twice. He had never introduced himself to her or mentioned his name to her.
Many viewers were given the impression (intentionally or not) that the shoe at the railroad tracks belonged to Luke or Molly. However, neither the shoe or clothing match what Luke or Molly had on when they were last seen. The series established the need to show any character's death to verify they aren't still alive. - This means the two children were likely still hiding within the prison when all the main characters ran away.
The train tracks have clearly been used recently since they're still shiny. This of course couldn't be that way since the apocalypse has been going on for a couple of years now and trains are no longer being operated.
Tara says that her sister was swarmed by walkers in the field. However, every shot of the field (in multiple episodes) shows no such feeding or bunched walkers. All the walkers remain spaced apart and continue walking to the main structure of the prison.