It will have some angle but don't think it's close to 90 degrees right?
do this - mark the length of sucking tube (clear tube) from the end equvilent to the length of dipstick, plug the clear tube into the dipstick tube. when the mark reaches the dipstick tube rim, going down further for about 2 inches. that is about reaching the bottom.
make sure the rubber end of the clear tube is firmly fit into the open slot on the top of the mityvac cylinder. (it has to be sealed well to produce a vacuum when you pump).
Additionally, check the bolts on the mityvac being tight. It could be loosen.
if still fails, return it.