Found the answer to this mystery. He was pulled by the coach for failing to run out a ball to first on a pop up. Another reason minors time is well spent. I was at the game and didn't even really notice it myself (although I was there with family and somewhat distracted), but that answers it. I just knew it didn't look like he was injured, and a mid-game call-up would have been odd.
As a side-note, it was the first time I saw Almora live and he was quite a bit smaller than I expected. Still very young, but it was something that stuck out.
I also have to say like Vogelbach even more now. He seems like such a down to earth guy, always smiling, spitting, frumpy and dirty uniform, joking with the umps. He definitely has a personality that reminds you of John Kruk. I'm not entirely sure his swing can make it to the bigs, but I'm pulling for him.