1) In the first part when the doctor says Seven has bullet fragments lodged in her skull.

These came from holographic bullets and while there are holo emmiters in sickbay and the rest of the ship was being converted the computer program was confined to holodeck 1.

this means that as soon as she left holodeck one i.e sickbay the ceased to exist.

2)In the second part there are two slip ups. First when seven is working on a grenade to turn it into a photonic charge she stands yup to throw it and gets shot dropping the grenade which then goes off it makes all the holographic weapons and soldiers disappear but not all the holographic road and sandbags etc.

Second when Janeway is running from the hirogen second in command she finds a holographic bermuda triangle where a soldiers legs are missing so she sets a trap she moves the soldier and lets the hirogen walk into the section when he goes to shoot her his gun disappears and she attacks him they struggle and the seperate she then bends down and pick up another gun (but she is on the other side of the split) she then runs through the split with the gun and manages to keep it and shoot the hirogen with it.