how to remove vinyl liner creases near jet and in the bottom of the deep end

How big a bubble are we talking? Can you post a pic?

And while it may not seem germane to you, knowing your chemistry reading might help us in determining the cause. Eg. Low ph can cause wrinkles in a liner...but so too can groundwater seepage or draining and refilling. If you have a good test kit, post up your readings:
fC
cc
Ph
TA
Ch

- if you don't, you might consider getting one to manage your pool the TFP wat at TFTestkits.net

How old is the liner?

Sometimes, correcting chemistry can help without manual intervention. If its water behind the liner, its also possible to suction it out, but I've never done it and would be reluctant to try to describe what to do given the chance it would run amok ;)
 
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