Starting with a USGS geopdf topo 7.5 quad, I extracted the layers to a spatialite database using ogr2ogr:
ogr2ogr -a_srs "WGS84" -f sqlite fisher.sqlite UT_Fisher_Towers_20170216_TM_geo.pdf
I then load these layers into a new map in qgis (2.18). Zooming to layer extent does not actually zoom to extent, but some seemingly random portion of the map. Same for zoom full. Zooming in with the scroll wheel sometimes zooms in, sometimes out. Panning with the pan (hand) tool can cause the zoom level to change. The scale shows 591,657,527 for multiple different zooms on the screen.
I've tried this on two different topos and have the same results. The behavior is the same whether I load one layer or all the layers in the map.
Not sure if it matters, but the ogr2ogr conversion/extract generates multiple errors, each of which reads:
ERROR 1: Max token size reached