With the cellphone, we saw him being chased by security. We saw him constantly on the run. He was on the move, so I guess he thought it didn't matter if they could find where he was because he was going to keep moving and keep hiding, he was so desperate that it was worth it. Really, what was the point of calling anyone anyway? No one could have helped him at that point, he was just in a state of desperation. It's like when someone cries and screams for help when getting arrested, there's really no purpose, it's pure emotion and panic, something people just do...not everything is justified and rational. When he spoke to his wife, it was because that was his wife and he needed to talk to her and didn't give a fuck.
As for not getting himself checked, I'll give you that one. It was a "WTF" moment. I could try to justify that by saying there are obviously tons of men who will avoid the hospital at all costs, they can have serious pain in serious areas or even twist their ankle and still prefer to wait it out, but it was a pretty odd decision on Wikus' part. The only thing I'd imagine is that he was afraid that he'd lose his position, or get in serious government trouble, for playing with alien technology instead of simply confiscated it so he prefered to wait it out in denial, hoping it was temporary. edit: He may also have feared people would take him as a joke, people already thought he didn't deserve his position and now he was so irresponsible that he needed to be hospitalized his first day on the job, so we're back to him pushing it off in denial and hoping it would be a temporary reaction.
Either way, I'm willing to let that go because the story did bring Wikus to the hopistal. It's not like they used his confusing decision as a way to avoid him ever going to the hospital, such as in Orphan where no matter how many pieces of evidence there were, the father would simply not believe that Esther was behind anything just so that they could keep the story going. You're right though, Wikus not going to the hospital himself is a "wtf" moment, but I wouldn't chalk it up to a flaw or reason you can't enjoy the movie.