Most ear infections are caused by the bacteria pasturella. This bacteria is commonly found on rabbits at all times--they are said to carry it at "sub-clinical levels", meaning there is a population of bacteria there that isn't enough to cause a full-on outbreak/disease. The rabbit's immune system keeps the bacterial population in check so that it stays at these low levels, and doesn't have a population explosion leading to disease. What usually happens with an infection that you can see is that the rabbit's immune system is compromised, by stress, an environment change, seasonal change, or another infection (such as E cuniculi). Then it can't keep the pasturella population in check, and the bacteria multiply. The greater number of bacteria cause an active infection, and you get the signs like pus, tilt, scratching, etc.
So, did Lego pick up Pasturella from Jacub? No, she probably was carrying it already. Could a stronger strain of pasturella, or one that is more resistant to some antibiotics have been transferred from him to her? That's possible. Could the stress of caring for and then losing her mate have put her immune system under stress, and allowed the pasturella that were already present to gain a foothold in Lego? Yes, that's certainly possible. She is in a fragile state, emotionally, and thus is also in a medically fragile state too. I'd keep a special eye on her, look in her ears for any pus, and do things to cheer her up and keep her healthy. Keep an eye on her food intake, give her a stuffed animal to snuggle with, spend extra time playing with her, maybe give her some probiotic.
It wasn't a bad idea at all to keep her and Jacub together--separating a bonded pair is probably more stressful than letting her care for him. Did she get a chance to see him after he had passed? Is she constantly looking for him? Some bunnies will do this if one half of a bonded pair is gone. Because most pathogens of rabbits are always present in their system, it's usually best to keep a bonded pair together if one of them is sick. I know it was comforting for both of them to be together, and by doing so you didn't expose her to anything that wasn't already present in her system.
