My print did not turn out as I expected. Where can I start troubleshooting?
first issue

bed inclination. it has to be heavy issue :)

if you have any other printouts then please reveal them so we could see if it's the problem

next issue

inversion of hole into solid object

i would say it's caused by wrong calculation of normal vector to some face(s)

algorithm uses normal to calculates what is "inside" and what is not

it's hard to say if it's an issue of 


object itself
application in which you modify it (even if duplicating or joining with other objects)
slicer engine


to fix the issue, you can try edit your object (recreate this hole)

but first - definitelly i'd align your bed properly ;)

EDIT

after closer look i bet it's the issue of bad object. it looks like pointed line is kinda remnant of some operations made on object in the past

in other words - it's possible place where normals are reverted and doesn't "create" inside but outside

all above this line is reverted. part of body disappeared and part of hole appeared

this is the issue for sure!