No, you haven't done anything wrong. The same thing happened to me when I first disassembled a M1900 bolt. I too thought to be completely familiar with Mannlicher-Schoenauer disassembly. The M1900 was just one evolutionary step in the development of the "Mannlicher" turnbolt from Louis Schlegelmilch's M88 German commission rifle through the Mannlichers M 92, 93, 95 and 1900 to the fully developed M1903 and later bolts. On all the earlier bolts, M88 to M1900, the bolt head is free to slip out and in of the uncocked bolt. The M1900 merely changed the connection of firing pin to it's nut from the former full thread to the 90 degree interrupted one, as you know. The proper procedure to disassemble these earlier bolts : Uncock bolt. Slip out the bolthead with extractor and ejector. Push the firing pin tip down on a wood block. Press in the safety flag. Unscrew and remove firing pin nut. Slowly release pressure so firing pin and spring slip out of bolt and cocking piece.
The main improvement of the M1903 and all later Mannlicher –Schoenauers over the M1900 was cutting the notch for the bolt head retaining lug on the opposite side of the bolt body. Only now the bolt head is captive and needs a half turn to release it after removing firing pin nut, cocking piece and safety.