This happened to me too, OP. I did "Molecular Level" with Minutemen, did "Institutionalized," then I decided I would join the Railroad and see their side of things after having seen the Institute's POV. I joined the Railroad fine, was given a ton of quests... and then when i returned, Desdemona started whining about my helping the Minutemen, and just repeats the same dialogue. Not only can I not turn in quests to her (I can't turn in Randolph Safehouse 1 and at least one other), I also can't warn her about the Bunker Hill quest the Institute handed me.
I CAN turn in quests given me by other Railroad members, like PAM, Carrington, and Tinker Tom.
I believe part of the reason is that if you side with the Minutemen, you have to turn the Institute hostile to finish the main story with them as your main allies. Whereas several Railroad quests actually requires you to remain friendly with the Institute, in order to infiltrate them. BUT.... it's not like you HAVE to turn the Institute hostile early--you can wait until later--so you should be able to do stay primary allies with the Minutemen and still help the Railroad for awhile. It's probably more likely an ill-timed dialogue loop.
I agree with you, if this issue is intentional programing, then if you can't do certain Railroad quests if you're primarily allied with the Minutemen, you shouldn't be given them. Desdemona's dialogue should also be way clearer and explicitly say, "I can't work with you any more unless you commit full to us," or something like that, rather than just repeat "please work with us instead" (especially since you STILL can "work with the Railroad" on other sidequests that don't have to be turned into Desdemona).
If it's NOT intentional (which it might not be given some people don't have the issue), it's a dialogue loop bug that needs fixing.