There are a ton of reasons.....

its possible your second flight is operated by another carrier so you cant check in on that one.

Its possible you cant check in for the other flight because its more than 24 hrs before that flight departs.

Its also possible your second leg flight got cancelled and you havent heard about it. Since the time of your booking they discountinued that route or they seriously redid the schedule. Had this happen to me with a Delta flight when they went through post merger with NW redoing their schedule and downsizing Cincinati as a hub.

Before your flight out talk with a gate agent to fix this.