Are these coming through the joints/seams between the boards? If so, the answer is simple. The finish seeped down into the seams/joints and wasn't completely dry before another coat was applied over it. As the floor expands, it pushes the not dry finish to the surface, where it does dry, forming poly beads. It usually happens more with OMU because OMU takes much longer to dry than waterbornes do. I have had this happen to me and it's a pain. The only thing you can do is either use water based finishes and make sure they are absolutely dry before coating again and follow manufacturer's directions on spread rate and dry times. Another issue in coating floors is one must control the temperature and humidity. I recall two floors where I didn't do this and both of those jobs came back to haunt me. After staining, the temps got high and dry and the wood shrank. I coated them anyway. Then the floors went back to normal as the temps returned to normal and guess what, poly beads
Also, use a faster drying OMU if you use one. Some brands, like DuraSeal, are much slower drying and are very thin in consistency and tend to seep between the boards more readily than some other brands, like Woodline.