Hopper complaint: $500 mistake made my Hopper!

I booked a one way flight from SAN-MIA.
My flight has a layover in DEN which isn’t unusual at all.
However what IS unusual is that I was given Two different ation codes for this itinerary.
Unsure of what that meant I continued my travel arrangements and began preparing to pay for luggage.
Frontier charges $69 for each bag (checked AND carry on) so my total was $240 for myself and daughter.
Then I realized because I have TWO DIFFERENT codes (PNR) I have to recheck my bags and pay TWICE at my layover location.
The ticket is with the SAME airline yet for some reason I have to Claim my luggage, pay and recheck my bags to get to my final destination!
Why do I have to pay twice for the same airline? I have no idea !
I reached out to frontier AND Hopper
Frontier says the issue is with Hopper since they made it under two different bookings so they cannot be merged.
Hopper says “oh well you received the ation email when you booked we can’t do anything to combine two different codes”
So now I have to pay $240 x2
For a ONE WAY ticket !!!
It makes ZERO sense and I’m disappointed Hopper has a nonchalant attitude as if they weren’t the reason for this issues.
I will never again use hopper or frontier at this point for this amount I could’ve gotten cheaper flights with carry on bags included with another airline.