Happens to me more often now too, even on the indoor trainer like the other night.
Best I can tell it's due to compression on the top of the foot impairing blood flow. If I keep the top straps loose there's less problem or no problem. Same with my walking shoes -- I need to keep the laces fairly relaxed along the top of the foot and cinched a little more around the ankles to keep the shoes from flopping around.
My feet are very narrow and bony with high arches, and most off the rack shoes are too large for me, so it's not a problem with shoes being too small. I use one or more insoles and arch supports to get the right fit (ProFoot Miracle insoles are the best I've tried, and much less expensive than the custom orthotics I used to get). I have similar problems with custom or appropriately sized shoes. If I wear thicker socks or layers I need to be more careful.
Compression socks can make it worse if I leave them on too long or they're too tight. I like the compression around my legs, but not my feet. If I wear compression socks at home or to bed it'll affect the circulation to my feet and the little toes go numb first.
I like simple Velcro strap shoes because I can reach down while coasting and adjust the strap. Often helps.
It's affected my pedaling style too. I can't really pull up much because with the shoes secured fairly loosely my foot flops around a bit. So I tend to stomp down on the pedals, pretty much the same as with platform pedals and no foot retention. I prefer clipless road shoes for the rigid soles -- helps reduce another problem, arch cramps.