I feel like over the past couple weeks several games I've been in have had short sessions. This isn't a problem. I'm going to say this game: this is NOT a problem. However, I'm not so sure the GMs themselves know that - at least judging by the number of times they've apologized for the short sessions.
To be perfectly honest, you can't avoid short sessions - at least if you care about flow - in your game. Why do I say this? because sometime something is going to take longer than expecter - through no fault of your own - or go faster than expected - again, through no fault of your own - and then you're left in this akward situation where there's 60 minutes left in the normal session time limit, but you just finished up one big thing and 60 minutes isn't enough to get started and to a good break point in whatever comes next.
Sometimes the group is just going to hit a point where everyone needs to stop, think, and let what happened in the game up to that point digest in their head. Forcing things forward is just going to result in bad play, and potentially out of character actions. Better to end at a point people are excited to come back to, in my opinion, rather than force things forward.
And sometimes you are just going to run out of prepared content. Maybe you had a busy couple weeks and couldn't get more done. Maybe you just couldn't get in the mood to prep. Maybe you were depressed, or sick, or hurt. Doesn't matter. Sometimes you run out of content.
So if you have a short session, don't beat yourself up for it.
If you find yourself consistently having short sessions you may need to review your game. Consistently ending the game before your scheduled stop time boils down to one of a few things: 1) you're not preparing enough content, 2) you don't have the stamina to run the game to the length you expect, or 3) your players don't have the stamina to game that length of time.
1 is the easiest of these to address. If you keep running out of content, you need to prepare more content. You can do this by either padding out your sessions with extra combats, or actually working in more content into your stories. I, personally, like to plan not only what is going on with the PCs directly (i.e. what plots the PCs were following last sessions) but also do light work for other things going on around the PCs. That way, if the PCs decide to change tracks, or wrap something up faster than expected, I at least have something ready to go.
2 and 3 boil down to the same thing. Some key part of your group isn't capable of playing for as long as you are scheduling. This isn't a bad thing necessarily. If you regularly burn out after 5 hours, maybe you should just schedule your game for 4 and a half. This way you have some leeway on bad days. If you can only go for less, than only run for less.
Short sessions due to stamina (which is just a blanket word I'm using for ability to maintain focus on the game ) is only a problem if the session length is so short barely anything can happen. Sessions as short as 2 hours work for some groups. Others get their regular dose of gaming in on the company lunch break in 60 minutes or less. You just need to be clear about expectations.
So please don't feel bad if you have a short session. But if you're having a lot of short sessions find the problem and fix it. Even if that's just telling your group you plan to wrap up around 9 instead of around 11.