In the Name of the Doctor Clara directs the doctor to take a broken TARDIS with a chameleon circuit on the blink.

Presumably this is the same TARDIS that the Fugitive doctor used. The fault predates the first doctor. The TARDIS would have been taken off her and would be in for repairs possibly scrapping after the doctor had their memory wiped and regeneration to the first doctor.

Therefore the Doctor took back the TARDIS the Fugitive used and the fault reoccurred. The sixth doctor tried to repair the circuit and again eventually it broke and reverted to the police box.

It's not that far a stretch of the imagination and I think this is the best explanation. Although there is still a lot of unanswered questions about the timeless child and the Fugitive doctor, hopefully the big finish series in production can answer some.