It's Nothing Serious but you Seem Incompatible
There hasn't been a serious disagreement between you, the lodger treats you and your home with a reasonable degree of respect, and isn't in arrears with rent, but still, you're not exactly the best of friends, and just about every little thing they do annoys you...
Is it possible that you didn't properly assess the lodger first (to make sure they were compatible with you and you clicked with them), or despite doing your homework, you just got unlucky, or you haven't had a lodger or even shared a house before (at least, not very recently) or could it be you simply aren't suited to sharing with a lodger fullstop (i.e. you can't let go and trust the person)?
For further tips on how to get along with your lodger, or to find a new lodger..(!) please see SPAREROOM.co.uk.
You might want to think objectively about what might be annoying you about the lodger - if it's something tangible, perhaps you can do something about it - for example - do you feel they're running up your bills too much? If so, are you charging them enough to cover it (remember, someone still has to live whether the rent is £200 or £800) so you need to take their lifestyle into account when deciding on a reasonable rent (but you can't raise the rent if you're in a fixed period on your Agreement).
Before you approach the lodger about the excess bills, be very sure that the bills have been run up by your lodger, and it's not a change to your own lifestyle or a new appliance, that you might have overlooked.
If it isn't bills, is that they could be a little tidier? Do they tend to hog the bathroom? Is their partner staying a little too often? Try to find at least one person who can give you an objective opinion - preferably someone used to house sharing (that is, sharing with house mates, flat mates, room mates or in a live in let - not just their immediate family or partner!).
So now you have a list of definite things that are annoying you. The second, and very important question is, are they breaking the terms of the Agreement (or understanding, if there isn't a written Agreement)?