Some will insist that "coyote" can only be pronounced "k+I ~ oat" (no long "e" sound at the end of the word). All dictionaries list both pronunciations, and vary on which is listed first.
Some dictionaries will phonetically spell a word like "bird" with two vowel sounds. Others will more precisely state that "ir" is one distinct sound phonetically spell it as "ir." It can be confusing to consider "r" a vowel and a consonant, but the minimal pair of "Earl" and "rural" shows that they are both. A common process in speech called dissimilation causes words like "library" to be pronounced "lie-berry" or "lie-bree." Other examples are "battery" pronounced "bat-tree;" "February" pronounced "feb-you-air-ee"
Dissimilation occurs with other sounds like "foliage" pronounced "fow-ledge." This process is specifically called disyllabic.
Assimilation is shown in the change of "t" to its voiced counterpart "d" when "little" is pronounced "liddle." The "g" is often dropped in the "-ing" suffix (compare the "n" sound in the word "in" and "ink;" "in+can" and "ink+can"). "Peculiar" has often been a one-word tongue twister for me.
Sometimes a part of a contraction will take on both the pronunciation and spelling of a similar sounding word. For example: "Could have" is contracted as "could've" and it's common to see this both pronounced and spelled "could of."
"Forte" means both a strong point and musically loud. Some insist that when meaning "strong point" it is correct to drop the "ay" ending, however, the pronunciation "fort" without the "ay" ending seems less frequent.
Should the ending in "genuine" rhyme with "win" or "wine?" It's just a matter of preference, style, or dialect. How the heck did we ever get "wenzday" our of "Wednesday?"
Are the "e" and "i" sound so similar that some pronounce "get" as "git" and "milk" pronounced "melk?" (note: "giddyap" is an alternative for "get up")
Sometimes it's just the stress that changes pronunciation such as "kilometer" pronounced either "kill-oh-meter" (stress on 1st syllable) or "kill-ah-mitter" (stress on 2nd syllable).
Then there will be those who insert a vowel between consonants like adding a "you" sound between the "c" and "l" in "nuclear." So instead of "new+clear" we hear "newk-you-ler."
One that I haven't seen a reference to, but I hear a lot is "prescription" pronounced "prescription."
My Algebra 2 teacher turned English teacher when we pronounced "root" like "book" instead of like "boot." She used the example of "roof" (like boot) being on top of a house and the other (like book) was what the dog says. A minimal pair for this vowel sound is "cook."
Miller Brewery tried to register the word "Lite" but was denied on the fact that words like "nite" and "lite" are standard variants. I didn't learn from their mistake, because when I tried to register "generalpages" I was told the phrase was too general?!
Speaking of midnight, when it is exactly 12:00 in the middle of the night, is it the day it was when it was 11:59 PM or is it the next day? Insurance companies rid themselves of that problem by stating that such and such policy expires at 12:01 AM!
Some archaic spellings tend to correct themselves like "sulphur" becoming "sulfer."