I have two alerts:

Factory Floor 33 has not enough logistics space
Factory Floor 61 has objects missing material for construction.

I teleported to 33 and placed a storage chest, but the message does not go away.
I teleported to 61: this is an empty factory which is stored in a chest somewhere.
There is nothing in it (apart from some water placed with waterfill).

I tried putting all the unused factories in a factory requester chest and blowing it up to get fid of them, but the messages still remain.

List of mods in use:

Aircraft_1.6.11.zip
AutoDeconstruct_0.1.12.zip
FNEI_0.2.7.zip
Factorissimo2_2.3.7.zip
Fill4Me_0.7.1.zip
Hovercrafts_0.17.15.zip
Krastorio-graphics_0.1.5.zip
Krastorio_1.4.34.zip
Nanobots_3.1.0.zip
SpaceMod_0.4.4.zip
Squeak Through_1.3.0.zip
Waterfill_v17_0.17.0.zip
aswil_0.5.15.zip
auto-research_5.0.2.zip
far-reach_0.0.11.zip
mod-list.json
mod-settings.dat
stdlib_1.2.2.zip

You might have multiple factory buildings sharing an interior surface. Check the map while you're in factory floor 33 to see if any other factory buildings are in there, same for floor 61.

To teleport into those other buildings you should know that factory buildings are spaced in a 512x512 grid on factory floor surfaces. So the second factory building on each floor is centered at {512,0}.