Getting charged honnery fee

Good day i am getting charged honnery fee for transactions that went through late even though i got the sms message saying the amount was allocated and reflected on the day i did the transaction 2 of which are for transactions that was made in april and getting charged honnery fee now only in June. Really what is the use of the sms service and why does the transactions go through if there is supposed to be no money in the account?