She is probably not picking up on his signals to go out. He knows better than to pee on the floor so he gets up on something elevated and then pees. Or it is possible he has a UTI or some other issue. It may hurt when he pees so he is trying new places to find somewhere it doesn't hurt. (A very common reason for cats who suddenly refuse to use the litter box but it can happen with dogs too.)
Males behaving badly
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We are having trouble with our 2 males fighting – one is new, one is old.
Almost 14 years ago, we started with our first Basenji, Brie. When she as 3 we got Ramsey, a male. Ramsey was always a happy-go-lucky guy without an ounce of aggression, even though Brie grumped at him often. She was actually the dominant one of the 2. Well, Brie took the sad trip to the vet earlier this year, leaving Ramsey. Soon after we got a female 4 month old puppy, Bonnie, to fill the emptiness. Ramsey has been ok with her, but mostly grumpy since he was use to Brie just sleeping ALL the time. He'll play A LITTLE, running laps around the house once a day, but mostly tells her to keep out of his space (still, if she invades his space, he'll just huff and walk away). Ramsey is now nearly 12yrs and Bonnie 11 months. Not wanting this cycle to keep going on, we added a playmate for Bonnie. Just over a week ago we added Smitty, a 9 1/2 month old male. He has a great temperament, respects NO, doesn't pull on his leash, loves to sleep on your lap, etc.
Bonnie and Smitty are pretty inseparable. At first Ramsey was OK with they younger guy, but they've had a couple fights. The first fight seemed like Ramsey was putting him in his place -- happened outside at the fence with another dog. But then once it happened over food. I had to pull them apart and both had been injured (Ramsey got a cut on his ear and Smitty on the snout). Since that fight, Ramsey has huffed and grumbled nearly every time Smitty is in his space. Again it happened when Bonnie and Smitty were playing inside and barreled into the old guy. Ramsey let him have it, Smitty held his own, and I pulled the 2 apart. So much for that first few days of them being OK together.
I tell Ramsey NO! when he growls at either one and will hold his nose if he doesn't stop. Never hit. I praise him when the other 2 are near by and he's chilled out. You can tell he looks nervous when they play. I also, now make sure I have my eye on them if they are all outside together and feed them with Smitty and Bonnie in their crates. I wouldn't say he is much more grumpy with Smitty. Before Bonnie wanted to play and would nip at his feet and drive us all nuts. At least now the "kids" can go play and leave Ramsey to sleep more. It has only been a week after all. Any other suggestions on how to keep some peace in this house?
Also, Smitty is still in tact, but that will change this week.
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Getting Smitty neutered should help some. Remember now is the crankiest time of year for basenjis…everyone is in reproduce mode! I agree with separating them at feeding time. At least until you everyone gets used to each other and sorts out their place in the pack.
To some extent, I think it is important to let Smitty and Ramsey work it out...but not to the point of drawing blood. Ramsey probably feels threatened by a new guy in the picture. I wouldn't be quick to reprimand one or the other for growling either. It is hard to know exactly what is going on during an interaction, and you wouldn't want to reprimand at the wrong time...kwim? If you step in and reprimand right as Smitty was about to submit, you could keep delaying (or escalating) the situation. If you think things are about to get out of control, separate and crate them both for a few minutes. Often that is enough for them to forget what they were angry about. I also do 'cooperative feeds' with mine when I am having an issue. Both dogs have to sit politely and I take turns feeding out treats to the offenders. But, beware...they need to be trained to do this first before you would want to try it with two animals that might fight over treats. It helps if you have another person to train and treat each dog when you first start.
Another technique that sometimes works is to simply get up, and step in between the dogs before things get out of hand. Usually, a stern 'knock it off' will help, if you can deliver it BEFORE they actually start fighting.
Good luck, I hope everything settles down soon.