Hello!
We just harvested our flow hive hybrid. Our first two flow frames went perfectly and then the third had bees flowing out in the honey during the harvest… at first it was just one or two then it seemed like almost every other second another need was pouring out the spout so we closed that frame up and stopped. When we checked the hive before the harvest a few days ago it looked capped. What could have been going on?
Hello and welcome to the forum!
Are you sure they weren’t in the channel already or getting into the honey after it poured out?
And also, once you crack the frames, it will keep on leaking out, realigning the cells doesn’t stop it completely.
Probably most of the honey would go through the leak back point and back into the hive but still there could be a fair bit of honey in your hive or tray.
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Hello and welcome to the Flow forum! 
One reason for seeing bees in the honey is that there is a hole in the bottom of the Flow frame. I would lift that frame out of the hive and inspect the bottom for a bee-sized hole, usually created by a small piece of plastic having broken off. Here is a post which shows you what to look for if you lift the frame out:
Thank you for the replies! I will check the bottom of that frame… they were definitely flowing out of the inserted spout… I was catching then with a spoon on the way out so they wouldn’t land in the jar! I felt so bad for them covered in honey! Would that happen if the honey wasn’t fully capped or something?
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It shouldn’t happen just from a lack of capping. The other thing that forum members have seen is that if one section of the frame is out of alignment, bees can sometimes get into the bottom channel. You can check that from the side of the frame, but it can be hard to spot. 