The words <said> and <says> are one of the two percent of English words that contain a sound that is a true exception!
It is very unusual for ai to say /ĕ/. I do not know when it came to be written and pronounced this way. It is probably that the pronunciation of these two words shifted over time. As with most English words that are true exceptions, these are two very old English words.
When teaching the spelling of this word to students, we find it most helpful to show them the parallels in spelling between lay-lays-laid, pay-pays-paid, and say-says-said. This way, they understand that the spelling follows a consistent pattern even though the pronunciation of one of the sounds breaks the rules.
We teach how the spelling of these words using spelling analysis.