I have a list of the Dolch sight words arranged by phonetic pattern, and also some of the reasons for a few exceptions, for example, "During the Middle English period, a certain type of angular writing was in vogue which resulted in some ambiguity for the reader when u was followed by an m, n, or u (sometimes written v or w.) Consequently, scribes replaced the u with o, and that spelling is retained in some words used today, e.g. come, monk, love, tongue, some, honey, son."
http://www.thephonicspage.org/On%20Reading/sightwords.html
One actually has an explanation, but it's long and not that interesting, and I like words and their history! I think are is just padded with an extra e, I'm not sure, many strangely spelled 3 letter words were "padded" with extra letters so they'd look better. Even when I know the explanation, young students don't seem to find it helpful. Explanations seem to help older remedial students and adults, they just run off my daughter's back like water. (She's 6.) In fact, she'll say, "Mom, just stop, please" if I start explaining things like this.
When taught phonics well, students are fine with exceptions. I do find it helpful to teach them in groups of similarly spelled exceptions when possible. "The ABC's and All Their Tricks" by Bishop is a good book that shows the most common exceptions from the most common 17,000 words in English. It has lists of words by their spelling patterns, with exceptions on the side of the page. It's worth the money if you're going to be teaching more than 1 child to read.