If at all possible I avoid taking "direct" routings to avoid this situation, I'll bite the bullet if I have to but not only does this sort of thing hurt your chances of an EUA, but you get nailed on the mileage too, as you are getting the mileage as if the flight were nonstop, instead of actual flown miles with two segments.

CO doesn't do a whole lot of this, but it does pay to keep on the lookout for these tricks if you are concerned with either your upgrade chances or EQMs for a certain flight. The biggest key is to catch direct flights on odd routings, like LAX-LIS, that CO does not operate, and manually construct a connection to cover your bases, otherwise you may be left with the sinking feeling that CO has just "pulled a fast one" on you at the airport, like the OP did.

Oftentimes, you can manually construct a connection with different flight numbers that work better, timing-wise, than the direct flight, which more often than not operate with different equipment.

Be ever mindful...