"Ends in" is acceptable in the sense that words can end in a vowel; end in an "a"; etc. This is often shortened to:
"Word" ends in "d"
"Ends with" seems to fulfill the same use:
"Word" ends with "d"
But I typically think of "ends with" using larger things than letters:
"This phrase" ends with "phrase"
"This is a sentence" that ends with "sentence"
Really, though, both "in" and "with" are doable:
"Hungry" and "angry" both end in "gry."
"Hungry" and "angry" both end with "gry."
The only difference I can find is their usage outside of words:
Our journey ends in Texas.
Our journey ends with disaster.
To directly answer your question, both work just fine in the original context. Some people prefer one over the other; some workplaces will have a strict style guide dictating which should be used. At the end of the day, consistency is more important.
As for references, there isn't much to find other than looking at hits via Google. NGram searching for "ends in/with c" shows:
But that really doesn't mean much, given the propensity for quirks in searching algorithms. Just browsing pages found by Google is of virtually no help given how often people use both phrases.