Both of my young cats are having diarrhea

I have two domestic short hairs, Jude (male) who is 10 months and Arya (female) who is over a year old. Arya began having the diarrhea first, a few months ago. We treated for worms with pills, neither cat received the full dosage that they were supposed to, I had tempted to put them in their wet food, but they weren't having it. So I went back to my vet and purchased some of the topical de-wormers. Then Arya started having blood in her diarrhea so we went back to the vet again (Mind you hers was started to get worse than Jude's awhile before this too, hers was much runnier than his, where as Jude's was just like mushy poop). Tested both cats for worms, even the rare one, Gardia or something I think its called (I had brought in a stool sample of Jude's) and everything came back negative. So I left there with another round of the topical de-wormer, some FortiFlora to help re-balance their tummy's in case there had been a bad batch of food, directions to put a teaspoon of pumpkin in their wet food, and pills to administer to the cats for three days to help stop the diarrhea. Their last medication of the pills was last night and I thought Jude was done with the diarrhea but I don't believe he is, neither is Arya. I was not aware that Jude still had the diarrhea earlier, because I went back to the vets and they gave me more pills for Arya to stop the diarrhea. I am becoming discouraged and so upset, I just want everything to be ok with my babies.   

They are behaving completely normal, drinking water fine, eating, playing, etc. Wondering if I just need to get another opinion, or keep treating them for the worms considering I know it is likely because they both have diarrhea, The vet did state that it is sometimes difficult to detect worms in loose stool vs a regular stool sample, so there is a slight possibility that the test results were incorrect. 

Any advice, or even thoughts of comfort would help at this time, it is hard for me to think about anything else recently and it is messing with my emotions bad. I greatly appreciate any and all responses. 

Also, the dry food that they eat is Wellness Core Indoor Formula and the wet food is Fancy Feast. 

Sometimes it is hard to detect things like coccidia and giardia in a stool sample because the cat has to be activly shedding it at that moment for it to show up. I would have their fecal test done again. No way this is "worms" after all that deworming. Giardia is treated with Panacur which is not going to hurt the cat to do a round just to rule it out. Coccidia can be treat with Marquis, but some vets use Albon. I would talk to your vet about dosing both cats with Panacur & Marquis to see if it helps. Something is being missed here if it is just not clearing up. They may need to send a stool sample to an outside lab to test for the rarer things that they can't test for in house. However, you may want to try another vet for a second opinion before you do that- any vet that says Giardia is "rare" is suspicious in my opinion? Giardia is VERY common. It comes from drinking dirty water usually.

I may be incorrect in the rare form of worms that she stated, the name may have been something different, but I greatly appreciate your response. I do have an appointment with them tomorrow morning to take Jude in, but I think I am going to try and drop off a sample to a different vet in the area and see if they have more specialized testing. Worms are the only thing that makes sense to me..the chances of them both forming food allergies to the same food, a highly rated food, is just so unlikely. 

Do your cats go outside?

Neither, ever. 

They do catch mice frequently though. About one every 3 weeks.