Agreed - it's not a glitch. You will get the proper EQM's.

However, you should be aware that COPA miles are a little slow to post to OP. In my experience, the base RDM and EQM miles take up to 10 days to post, and bonus EQM's take up to 2 weeks. The 50% bonus will post at the same time at the flight miles, and the 25% bonus will show up a little later. You will get the 25% bonus on the 50% (i.e. total EQM's posted will be 187.5% of base miles).

EDIT NOTE: In my original reply, I said that I did not know how the 50% bonus worked, since I had never booked Y. I had forgotten that I had done so just this past August, and the info above reflects how the miles were posted for me.

Further, the bonus miles for different legs don't always post at the same time. On my last trip, the bonus miles for the second leg of the outbound posted a week before the bonus miles for the first leg.