Well, the author doesn't have to, if they don't care about their story making no sense
the story doesn't necessarly "make no sense".
It can have multiple interpretation, some sensible, other not, depending of how you "fill" the holes, the unanswered/dubius issues
1.does the catalyst fully and directly control the citadel (as spece station and as mass relay)?
A) yes
b. no
2. does the catalyst fully and directly control the reapers?
A) yes
b. no
3. What the catalyst is telling you about the synthetics being a threat for all organic life is
A) the ontological truth
b. what he believes being the truth
C) a lie
D) what the crucible is forcing him to tell you
E) ....
The catalyst is helping you (instead of waiting/commanding the reapers to blast the crucible) because
A) his solution won't work anymore (as proved by refusal ending)
b. because he's forced to do so by the crucible
C) you're indocrinated, that's a meta-intellectual boss fight, pick destroy!
D) ----
You can combine the various option is ways that makes sense (1B - 2B - 3B - 4A; or 1A - 2A - 3D -4B); and other ways that doesn't make any sense, even if, taken one by one, the option can be more likely than other.