Mares have been running with stallions but still showing signs of season?

Yes, mares sometimes show signs of season even when they are pregnant. I had a pony mare who got in with a long yearling colt once. (He was scheduled for gelding 2 days later). She came into season throughout her entire pregnancy - by the time we knew she was pregnant, it was far too late to do anything about it.

Who is handling the breeding? A mare is at her most fertile when she shows the very first signs of heat - signs so subtle only a stallion would know. If the mare is "put to" the stallion when someone unskilled finally notices she's in heat, it's probably too late.

If they simply kick and stand, they're probably not at the correct time of season. They may just not like the stallion for some reason; it does happen.

Are you hand or pasture breeding? If you're hand breeding, you'd know if the mare was ever covered. If you're pasture breeding, you can be reasonably sure she has been.

If the mare has been covered multiple times or has been turned out with the stallion, I would have her scanned. The mare who's only shows signs of season occasionally I would definitely recommend scanning.

If these mares have been covered and aren't in foal, you need a vet to check them - preferably one who specializes in repro. Many treatable conditions can slow or prevent conception; some of these conditions can infect the stallion covering him and endanger him as well. If you have not had a repro check done on the mares, you should - it should be done before you even turn them in with a stud.

I would get them vet checked to be sure. Some mares do show signs of seasons. We have had some mares re checked. They could have other reasons for not getting in foal. But without getting checked over you wont know.

Now I am persuming you have had your mares swabbed and blood tested before you put them to the Stallions.

Some maiden mares will not stand unless held. But your experienced mare should stand (unless she has been held for cover)

The mares may need to be checked for infection. Also, do the stallions ever get their private parts cleaned? This should be done regularly, even for field breeding. Poor hygene will creat infections that are not necessarily apperant to the naked eye.