It would appear you have crossed wires.
The three lighting circuits should be totally independant but in your case there not.
The three circuits will have three switch cables (2 core and earth) in addition to the 3 core and earth needed between a couple of 2way switches.
The switch cable relating to the 2way circuit could be fitted at the other 2way switch so at the switch in question you may only have two switch cables.
There is a further alternative regarding the switch wires where you could have the red wire feeding in at one of the 2way SWand the black leaving at the other SW but this is not practical and highly unlikely
You need to establish first, where is the switch cable for the 2way circuit.
I suspect it is there at the switch in question and I suspect the black from this cable has been crossed with a black from one the 1way switches
Connection for cable between 2way switches
RED runs from COM to COM
BLUE runs from L1 to L1
YELLOW runs L2 to L2
Connection for the switch cable to one of the 2way switches
RED runs to L2
BLACK runs to L1.
All these wires should be identified with a red flag of insuation tape at each end to indicate they are 'switched live'(well not the red ones)
Altough I have ignored earth wires you must not