Yes it is paid in arrears, normally 4 weekly. If they pay the full rent then it should work out the same over a lengthy period as receiving monthly payments in the normal way.
But what is happening is that - if you have a normal tenancy agreement which specifies the rent is due monthly in advance - there are always arrears of rent, when compared with the agreement. When the tenancy ends the position should correct itself.
Theoretically you could demand that the tenant pays money to bring the payments up to date in accordance with the tenancy agreement, but if such payments are not made you would have difficulty doing anything about it. You would have to start a Court action for possession and it is by no means certain it would be granted, particularly as the amount you are talking about is small.
In my view, if you are otherwise satisfied with the tenant it is far better to let the present arrangement continue.