I don't know how many ep's you've seen, so this may contain some spoiler information ....
I agree that they should be honest with each other and Max leading Logan to believe that something was going on between her and Alec was wrong, but I understood why she did it.
She cares about Logan so much that she doesn't want to hurt him, and that is the reason she is not honest with him.
As for the virus, yeah it is starting to get annoying, but at least in the finale, Logan finally figures somethings out .....