Is my employer responsible for the bank fees caused by their insufficient funds?
Legally, yes: if it was the employer's fault, such as due to not having sufficient funds (as to it being the bank's fault, such as due to some processing delay) that your purchases and payments did not clear, they would be liable for the bank fees you incurred; people and businesses are responsible for the costs they cause others through their negligence, or unreasonable carelessness, as well as by breaching their obligation, such as to pay wages and salary on time. Practically, if the employer will not voluntarily reimburse you, you'd have to sue them for the money, which may well not be worth doing.