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I assume the routing isn't through the same connecting airport. If so, that would impact the fare along with things like seat availability.

It's not "the same flight" if you're looking at different layover lengths. There may be less inventory on one of the segments with the longer layover, you absolutely cannot just take a single datapoint and conclude "they're doing this on purpose just to screw me over" give us a break.

If it is the same connecting point for both options, then it is likely married segment logic availability. This has been around for a long time and not uncommon. You can try calling res, but breaking married segment logic is almost impossible.

you realize that if you book the shorter yet legal connection and you misconnect that they don't just leave you stranded at your connection point, right? they'll put you on the next flight. And that you're probably still like 90% or greater to make the 1:15 connection.

Has the OP looked at fare class availability for the individual segments as well as for the through journey? If one of the segments is more full, it's not surprising that tickets using this flight would cost more.

If there is a seat still available.

sure, but as a DM (which this poster in question is), my success rate when standing by for oversold/overbooked flights is 100% (and I do it a lot). It's obviously not guaranteed, but nothing is, and the chances of success are way, way better than most people assume in these cases.