Taking the discontinuity guide from the BBC Dr Who Classic Site:

The Invasion of Time: Myths

Although three Sontarans are seen to enter the TARDIS, only two are killed, meaning that there is still a Sontaran lost in the TARDIS somewhere. (Only two Sontarans, Stor plus a trooper, are seen to enter. The trooper is killed with the de-mat gun, and Stor is also eventually killed with the same weapon, but outside the TARDIS.)