For some reason it when I try to go down the hatch into the basement in the Toll House it I go into the basement it flashes a couple of times and then I'm back on the upper floor where Anders sword of Tyr is at
Same here; also with the necromancer's basement in the Blighted Village (though I did get there eventually after a few tries).
Yeah, you should report that issue via the Launcher page. Took me a while to figure out a workaround. After patch 3 when you click on stairs and the like the game wants to click again. Click on the ladder and then *very* quickly move the cursor to the edge of screen, that will prevent the second click that brings you back up the ladder.