Crossbow bolts are much shorter than arrows and many times heavier, and are not typically fletched. Bolts can be made completely of metal, also, whereas arrows universally had a head, a wooden shaft, and fletching.

This seems like more of a linguistics/etymology question than a historical one.

It appears that in olden days the word 'bolt' referred more generally to arrows of any sort, as James Mitchell's Significant Etymology notes that Chaucer uses the proverb "to shoot a featherless bolt" (meaning to labor in vain) - but the contemporary definition of a bolt has it that they can't be fletched or feathered. (This, incidentally, causes fierce arguments over whether modern hunting crossbows shoot bolts or merely arrows.)

Additionally, the Online Etymological Dictionary states that 'arrow' was a rare word at one time, and other words that have disappeared from English were typically used instead; perhaps those other words were simply replaced by 'bolt' and 'arrow' in different contexts.