Do you remember how you ended up getting on that flight?
This is what the logistics look like today for the two cases:
I. (I bought the direct flight)
A. Show up at the airport and check the board for a Republic flight from Detroit to Houston. Learn from the board where the checkin counter is.
B. Check in at that counter ("Final destination: Houston") and be issued a single boarding pass showing the boarding gate.
C. Show up at the gate, which displays information about the flight, including a final destination of Houston.
D. Board.
II. (I bought the cheaper flight with a layover)
A. Show up at the airport and check the board for a Republic flight from Detroit to Memphis. Learn where the checkin counter is. (They're both Republic flights, so this will be the same counter.)
B. Check in at that counter ("Final destination: Houston") and be issued two separate boarding passes, one for a flight from Detroit to Memphis and another for a flight from Memphis to Houston. Only the first one will have a gate number on it.
C. Show up at that gate, which, like the flight board, shows that the flight will be going to Memphis.
D. Board.
The flight number on your boarding pass wouldn't matter, because you'd be trying to board a flight to Memphis using a boarding pass that says you're flying to Houston.
What was different then?