I bring this up because usually Nintendo is pretty explicit with how long their presentations will last, whether it be 4, 12, 20, or 45 minutes, not matter what stretch of time it is, they always say in advance. So when watching today's Indie Showcase I was a bit surprised to see that the presentation ended pretty abruptly right around the 25 minute mark when it was advertised as being a full 30 minutes. You can even see on their YouTube channel, the full presentation clocks in at 25:17. It feels like something almost had to have been cut last minute. Was there going to be a Castle Crashers segment? Was an indie character going to be announced for Smash (unlikely)? Did a game have to be delayed? 

Did anyone else notice this and find it strange?

Maybe they were going to announce the release of Joker for Smash and the next (indie) challenger's release date? I wouldn't be surprised if they wanted to do both at the same time, but left it for a later date due to Joker not really being an indie character.

Maybe Ori and the Blind Forest? It was rumored to be on Switch alongside Cuphead.

Maybe they were going to show Mother 3, but somebody accidentally deleted the code to the game last night without a backup and they removed the trailer?

That's what I'm thinking as well.

I think they cut Mutant Year Zero since the port was announced shortly after. I don't think it was Steam World Quest despite it also releasing a new trailer since Nindie Directs focus mostly on American indies

I noticed too, OP and thought exactly the same as you. As to what was missing i could only speculate and tbh i have no idea!

Quite possible. Not only was it too short, the ending was pretty abrupt imo - as if the last one was cut out.