Make good the wall, use longer screws into solid wall or fix bracket to good parts of wall.
It's not usually that critical to line up.
Is the downpipe holding the cistern at the wrong height or to the side or if no down pipe have you screwed it to the pan crookedly?
its a closed couple toilet where the cistern sits on top of the pan. The cold water feed is a fixed pipe with an iso valve. The cistern has to be bang in the centre to ensure the cold water pipe can be screwed back to the end of the float valve. The nut is ending up being tightened at an angle and so there is a risk its not a secure fit - possible to end up with a leak since it would mean the washer inst being compressed adequately.
I was thinking of fitting a short flexi hose to the cold water pipe but there is hardly any room for that - as the pipe comes out of the wall its got the iso valve and from iso valve it angles up 90 degrees, approx 10cm into the cistern.