Layout operation messes up the left margin of system

Please share the score

Indeed, we'd need the score to do more than guess. But my guess is, either a symbol that needs to be aligned to the start of the measure was dragged out of position and MuseScore is trying to make room for it, or else the clef segment has a leading space adjustment manually applied (perhaps you accidentally dragged it). The former you reset by selecting the measure and hitting Ctrl+R to reset positions; the latter by selections the clef and hitting the reset button next to the leading space control in the Isnpector.