At the start of the episode it is stated that the discovery of two dead crewmen accounts for all the missing crew. But during the battle we see at least three crew members ejected into space. These three would have been lost and never found (Ships sensors were out after the attack) meaning the entire crew could never be fully accounted for.
Archer tells Degra that they were able to enter the first sphere they encountered because it was damaged. In Anomaly (2003), in which they first came across a sphere, the shuttle crew found a hatch which failed to open when they hailed it so they fired on it and this caused the hatch to open.