Roommate issues?

I'm trying to be helpful here, but you're coming across as way too dismissive of Haley!  Sure, weekly meeting is a bit over the top, but agreeing on house rules is MANDATORY!  A lot of us living for the 1st time on our own with roomies learn this the hard way.  So this reads like Haley might have handled it wrong, but her basic instincts were spot on.  I also don't get why you dismissed her concerns about a guy spending the night with Linda.  It might not bother you, but it would bother me.  In fact, this was the same issue the 1st time I had to deal with this.  The door might be closed, but it can open unexpectedly when you're standing there half naked.  Now that a situation has arisen that annoys you, it's kind of puzzling you still don't see the problem.  

If your lease isn't ending soon, it's obvious the 3 of you need to have a chat about all this.  Overnight visits are always the biggest problem area, but they aren't the only one.  I also think when you suggest this you need to start by apologizing to Haley for dismissing the idea without thinking it through.  I say this because if you don't, you'll look like a hypocrite when you now decide it DOES need to be talked about.

Also, this doesn't have to be argumentative or anything.  I've been in this situation twice with different people, and both times we had a similar solution.  Nobody spends the night on weeknights.  On weekends, it's more of a free for all, but guests must be gone by Sunday afternoon.  Other rules that make sense are that a bf should never be in the apt without his "person", and guests should never be given a key, even temporarily.  These situations often devolve into this and it becomes a big mess.   Another rule that would help you is that if a tenant needs the kitchen while a guest is in there, all she has to do is say so and the guest vacates it.

Finally, when you say you thought the 3 of you are old enough to not need rules, this is wrong.  I moved into a fun group home when I was 30, and I can assure you that the 1st thing we did was set house rules.  

Sounds like setting the rules (or boundaries) early on, wasn't such a bad idea afterall.
You say Linda is rarely home but as you and Hayley work from home, you see more of each other -  maybe start by acknowledging that sharing a flat has been a new experience for you, apologize for dismissing the idea of weekly meetings and Hayley's feelings when she stated she didn't like Linda's boyfriend being around so much... discuss how things are going & consider the option of having a catch up every months... discuss stuff like cleaning, jobs that need doing, how X is or isn't working and any issues & discuss the use of the kitchen and having boyfriends stay over. Having a clear understanding helps. 
Good luck. 

Sort of funny, guess you should have gone for those house rules after all. Everyone has rules, or their pleasant little lives, get invaded. Live and learn, just as you are now. Time for you to call a house meeting, maybe suggest some rules and times for this sort of behavior. Your personal feelings are actually the difference in how you feel now when comparing the two roommates behaviors.

Maybe it's time to have some of those weekly meetings you're not going to need and establish some of those rules that are too strict? 

Come to a general agreement about guests. Should everyone do their visiting in their own private area, as much as possible keeping guests out of shared areas like living room an kitchen? Is there a curfew on guests, like they must be out by midnight, may arrive no earlier than 8? Are guests allowed to shower? Shave? And while you're about it, does anyone feel that someone isn't cleaning after themselves in the bathroom? 

This girl, Haley is the one wanting to make strict rules but then seems to be the first one to break them. You (and any other flat mates) need to have a word with her and remind her that the rules apply to everyone - not everyone except her. It might be a good time to be looking for different accommodation, without Haley.

A wise person sees red flags or possible warning signs well in advance sometimes and protects themselves by setting rules when it comes to roommates especially because you dealing with different people attitudes personalities lifestyles etc. Rules are made to keep order regardless of where you are at or who you dealing with otherwise as you are finding out the hard way where there is no real communication plans fail chaos follows. Only thing you and your roommates need to do now is schedule a talk time together to pray this all works out better in the long run. Always know who you dealing with. Bad association spoils useful habits or corrupt moral standards and can destroy friendships relationships your peace of mind and cause division. 

Tell "Sheldon" to go fudge herself.

Guess you should have listened to Haley when she wanted to set some rules for this place.