Hi Kelly,
Sorry I have not come back to you it was late!
Guppies are known for being picked on as they are slow and have tasty flowing fins. How is your betta? If he is untouched I would guess him to be the culprit.
Guppies are not especially long lived and if they have been in your tank since the beginning and gone through the cycling process then they may have been weakened anyway so maybe they were unable to heal.
I can't give you any advice except for looking at your stocking and consider taking the sepaes, guppies and the betta male or females back or finding someone else to take them on. You then need to up the number of shoaling fish like danios and tetras to at least 6 so they will be happy. Do it slowly so as not to overload the filter. Possibly the loaches too, although you don't say what kind you have - zebras or yoyos should be fine but clowns will outgrow your tank quickly.
I am sorry about your guppies, we have all fallen foul to bad advice from the lfs...in future make sure you come here and research the fish before you put them in. This website is great, ots of very friendly knowledgeable people come here and help to advise, and I am so glad I found it, it had saved me many a time.