Although an employer is to take into account in the calculation of withholding the number of withholding allowances that you specify on the most recent Form W-4 that you've provided to your employer, there are various methods that the employer can use to calculate the withholding that can result in possibly differing amounts of withholding for a given amount of wages per pay period. Wages that vary from pay period to pay period could also result in a varying percentage of withholding due to the way withholding is calculated. (Withholding cannot be specified to be a particular percentage of wages.) I wouldn't expect an employer to constantly vary the choice of calculation method, but I don't see anything in the IRS guidance that explicitly prohibits doing so.
See Chapter 9 of IRS Pub 15-A: https://www.irs.gov/pub/irs-pdf/p15a.pdf
Being paid supplemental wages such as a bonus can also substantially affect the percentage of pay that goes to withholding for a particular pay period depending on whether the employer chooses to report the supplemental wages combined with regular wages or report the supplemental wages separately subject to a flat 22% federal withholding rate.
