Misalignment when generating centroids with QGIS

QGIS does not reproject data on the fly automatically. It's not unusual to have a Coordinate Reference System (CRS) defined for a project and have data added to the map with a different projection that displays but has not been transformed to the CRS of the map. If the CRS of the map and the CRS of the data are close enough, the data will display but be in a slightly different position.

Your centroids and polygons are in different CRSs. The solution is to either:

• project one of the datasets into the same CRS as the other or
• check the "Enable 'on the fly' CRS transformation" box on Coordinate Reference System (CRS) tab of the Project Properties window.

Be aware that the second option does not affect your data, it only projects it for the display. The underlying data is not changed.

You just need a new QGis plugin to create polygon centroids, you can check out "Centroid Maker" from here

edit: It is more efficient/accurate for the problem of "island" geometries, which confuses traditional centroids makers.