Hi.
I think JoomShaper has nothing to do with it.
Such a problem can only be because of a user error.
And here it is

Never use negative margin (and any margin at all) in the main blocks of the layout. Any manipulations with DOM elements need to be done inside but not outside of such blocks.
If you explain what you wanted to achieve this, I can advise you another decision that will be correct in this case.
I believe that this code would be useful to you instead of footer/bottom sections negative margins
#sp-bottom .sp-module {
margin-bottom: 0;
}