On Berachot daf 2a, the gemara says that we have two berachot before Shema and one after (in the morning) and two before, followed by two after (in the evening).
As far as I'm aware, there are three berachot before Shema in the morning:
- Yotzer Or
- Yotzer haMeorot
- Habocher
On the other hand, in the siddur of R' Saadia Gaon, the former two berachot are combined in a single paragraph, unlike our modern siddurim.
How do the gemara and meforshim qualify this inconsistency?