Here's a tip in case you ran into the same problem I did.

In the Mausoleum, you have to defeat the eight skeletons, use the Magic Bottle to collect their souls, and deliver them to the central area. I delivered 7 before heading to the white soul in the top left--and the soul just wouldn't enter the bottle!

There's a simple solution--leave the Mausoleum via the little door up top, and then re-enter. I was afraid everything would reset, because the skeletons come back if you leave the Mausoleum. However, I found that they do come back but any souls you've delivered remain in the central area--so no repeating all your hard work!

(I presume everything won't reset if you leave by the bottom door instead, but I haven't tried that.)

I re-defeated the skeleton with the white soul, and this time it went in the Bottle.