There is no documented indications bearded dragon females change color indicating they are gravid... However, a constantly dark beard and dark overall coloration is more a sign of illness, stress or other health issue.
If the male is in with her still, remove him. Reassess your husbandry (double check temperature, air and basking, cool side too) If the UVB bulb is old, replace it with a new one...Also, how long was the last copulation you observed? If you normally kept the male separate and only introduced them for mating..how long since you introduced the male?
It is possible she is close to egg laying and this is causing her to feel stressed...especially if there is no suitable egg laying bin accessible to her. Has she been digging alot? What is her current behavior, other than darker colors?
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PHLdyPayne
Forum Princess