No contraceptive is perfect, and the rates vary between methods. Note that some of the methods in the table can be combined (and often are), thus lowering the overall chance of pregnancy.
ars's comment seems a bit extreme; while condoms don't perfectly prevent pregnancy, they are certainly quite effective at reducing the chance of it.
For a situation like this, with (according to geertj's calculations) 40% chance of severe birth defect, that's far too much.
Condoms are not the solution here - in fact I think they do more harm than good because people think they work (like you did), while they are not sufficiently effective.
Result: When used consistently and correctly, condoms are 98% effective in preventing pregnancy and are the only form of birth control that also can prevent STIs.3,7,8 This is why it's important to follow directions for correct use.
Somebody is lying.
So in essence a condom works if you use it and if you don't use it and get pregnant it is not very effective. WTF? At this point I'm cursing for wasting my time.
"Perfect" use increases effectiveness, but even if you aren't just derpy about it, they can still fail.
I routinely see this assumption that birth control works perfectly if you just use it, and that simply isn't true.
The point is that if you have an entire population of people who say that their primary method of contraception is male condom, you should expect an unplanned pregnancy rate closer to ~18% per year than 2% per year.