Why do I measure 5V in this circuit when I should measure 3.3V?
The linked schematics does not seem to be exactly right one for the board.

There are no R25, R26 on it. Since both are just jumpers, and R26 is located right next to LDO and R25 is on connector pin 13 marked "VDD5V" on schematics, I suspect they (or at least one of them) are used to bypass LDO.