Crank extractor not screwing in properly
If you want to save the cranks, consider taking this to a shop.

Wonder if this bike was run without a plastic cover over the hole?  

I suspect the threads in the crank are slightly damaged.  You might be lucky and force the extractor in correctly, or you might screw-up the threads completely if it on the wrong angle

An LBS will have taps that will chase the threads back to smoothness.  Taps like this are quite expensive and generally unnecessary for the home mechanic.  I don't own any this size.

You can try another crank-extractor - I own two and they have subtly different tolerances.  Not sure how that works but one goes in where the other doesn't, and its not always the same one that works.

If the cranks are trash already, then slap a lot of lube in  and have your best effort at lining up the extractor.  Your last resort is to carefully cut the crank off by grinding through the eye, without going into the BB.

If the BB needs replacing AND its the left side, you might be able to grind through the BB axle between crank arm and BB, and then use a drift to push the stubby bit out of the crankarm eye.  This should save the crank arm but it will still have damaged threads.  If its the right-side then the spider and chainrings will be in the way.