You Need to Change the Agreement - and NO COMPROMISE!
But supposing you are not prepared to compromise, even though you originally agreed to whatever it is that's now an issue for you? Before you approach the lodger, be honest with yourself - is it really just this one thing that's annoying you or causing real difficulties for you, or is it that, at least at the back of your mind, the lodger has outstayed their welcome and you'd really like them to go? You need to be absolutely sure that it really is only this one thing that's bothering you, otherwise, once that has been resolved, you will then find something else annoys you, until the relationship with the lodger breaks down completely see ...Lodger and landlord incompatible.
If you're within a fixed term, and your Agreement specifically grants whatever privilege you want to withdraw, you will need to be prepared to pay compensation to the lodger, to either forego the right granted or move out early, or otherwise put up with the status quo until the fixed term ends.
The most decent thing to do is again have a friendly chat, perhaps over a meal or coffee, not by button holing the lodger and trying to explain in five minutes. Accept responsibility for not having thought things through more clearly from the start, then say something along the lines of, "I'm really sorry, but x is making me very uncomfortable/making it difficult for me, etc, and I can't live with it, and there's no compromise that I can make on this" - NOT "I'm not prepared to compromise on this."
Obviously, it depends on what it is, and how much impact it will have on the lodger's life - as a rule of thumb, is it something that someone would reasonably expect to do or have in their own home? If so, then there is likely to be quite a bit of resentment on the lodger's part - if they don't have much choice but to stay with you, they may well put up and shut up, but things will be strained...
If you are going back on something in the Agreement (or your understanding) and you're not prepared to give way to the lodger on that particular point to any degree, especially if it's something that might be important to them (and if it's something they're doing or using a lot, it may well be, or will at least be something they've come to expect), it will be much better if you can offer the them something else by way of compensation - can you give them a rent reduction? Extend the term of their contract (if applicable)? Offer them exclusive access to part of the house e.g. they can have the lounge to themselves one evening each week? Take over your parking space? This also lets them know that you're not simply trying to get rid of them "via the back door..."
For further tips on how to get along with your lodger, or to find a new lodger..(!) please see SPAREROOM.co.uk.
Whether or not it's possible to compensate the lodger, they may decide to move out - in which case, let them decide on the notice - if they want to move more or less straight away, it's best to let them (and don't charge them the rent for the remainder of the notice period!) or they may need a bit more time to find alternative accommodation than was originally agreed (as this will most likely come as a complete surprise!) in which case, allow them a reasonable extension to find, view and make the practical and legal arrangements to move - I personally couldn't see this taking less than a month. You might also allow them to keep any possessions at your place for a few weeks until they're properly settled - even for a small amount of stuff, which doesn't include furniture, the logistics of arranging removals and couriers can be a nightmare, especially if the lodger doesn't have a car!
If they accept your amended Agreement (perhaps because they have no choice!) don't expect the relationship with the lodger to be anything but cordial, and if that person was your friend, you're very likely to lose that friendship - even if they can't tell you at the time, as they need a roof over their head!
I personally lost what I thought was a very good long term friend over this very same situation, so tread very carefully before charging in and demanding that the lodger concedes rights you've previously granted...
Lastly, if the lodger is staying (even if you don't have a written Agreement) write a friendly email, note or letter to them, summarising your amended Agreement or understanding and include the date of your discussion. Be sure to thank them for their understanding and for complying with your needs. If you have a written Agreement, attach a copy to it.