Absolutely.
The whole process is automated:- add capsules into one hopper, the powder fill into another, and the capsules are filled and closed automatically.
The bulk is then taken to the packaging line where the plastic blisters are formed, filled with capsules (at this point there is a light sensor to check that the blisters have been filled), then sealed and packed into cartons.
Obviously, there are QA checks in the process, but there is no requirement for the capsules to be all one way...
The different colours used are for identification - the combination of size, body colour/cap colour and printing (if any) is registered and is intended to assist identification of the medication and there are tables to do just that.
(similarly for tablets - e.g. Warfarin - comes in 3 strengths 1mg, 3mg, 5mg - all are the same dimensions, but are colour coded brown, blue, red respectively to assist identification)
HTH
Colin