And with games against Liverpool, Arsenal, Manchester United, Tottenham, Chelsea and Manchester City to come, Hughes will fear for his side's chances of survival.
They did enough to win this game and were the better of the two sides but, if they are relegated, may see Hill's disallowed header as a pivotal moment.
With the scores level at 0-0, Hill's header would have shifted the momentum QPR's way but instead it gave Bolton a lifeline.
Steve WilsonBBC Match of the Day commentator
A huge victory for Bolton and a really damaging defeat for QPR. What a lucky result this was for Bolton because Clint Hill's header crossed the line by about two feet before Adam Bogdan pushed it on to the underside the of bar. Rangers and manager Mark Hughes will be incensed.
For Bolton, this result was their first win in five, and could also prove crucial in their attempts to beat the drop with Owen Coyle's side now a point above the bottom three.
Just two points separated these two teams at the start of play and the first half was evenly balanced.
Bolton had the first real chance of the game with David Wheater's header from Miyaichi's corner headed off the line by Bobby Zamora.
Soon after, Zamora was in action at the other end crashing a half-volley from a tight angle against the crossbar following a floated pass from fellow striker Cisse.
The controversial incident arrived 20 minutes into the game with Hill denied a goal when his header from Joey Barton's corner clearly crossed the line, before goalkeeper Adam Bogdan palmed it on to the underside of the crossbar.
Hughes angry with officials
However, with the assistant referee unsighted and referee Martin Atkinson unsure, Hill was denied his first Premier League goal, on his 400th career start.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.