1) The phaser was fired after the transporter was activated, which proves that Will could not have fired.
2) They could have easily examined whether Will's phaser was fired, but didn't.
3) Will claimed he made arrangements to stay overnight on the planet, but they didn't check.
4) The Krieger waves could not be duplicated on the holodeck.
5) Troi didn't sense any deception when it was obvious that there was.
6) Apger's testimony (as given through his assistant) conflicted wildly from his wife's. This casts doubt on both their testomonies.
7) Geordi (who was also on the station) gave no testimony.
8) They just could not think of any way to use the holodeck that didn't threaten the ship.
Rubbish from start to finish.
Rubbish from start to finish.