In my (admittedly not that large) experience, hand-applying paste with a stencil is much more likely to end up in excess solder paste than if it were being done in a paste printer. No surprises there. So here’s factors to consider, and how to mitigate them:
As others have said, avoid multiple passes. What happens, especially if the stencil is not 100% flat, is that paste gets squeezed under the stencil. Then on subsequent passes, the solder balls on the underside raise it up a tiny bit more, so even more paste gets squeezed. And the pressure of subsequent passes spread the paste.
What’s even easier to forget:
any subsequent first passes will also be affected. Any time you have smearing, clean the stencil perfectly before using it again. And be sure to do this on a perfectly flat surface to make sure you don’t bend the stencil at all, as even the tiniest dent will cause smearing.
Make sure one edge of the stencil is taped down such that it acts like a hinge so you can lift the stencil up cleanly.
Once you’ve lifted the stencil off a print, DO NOT lower it back down! This easily causes smearing.
Stencil thickness is another factor. For a given aperture, a thicker stencil will obviously deposit more paste.
Finally, aperture size: the openings in the stencil are NOT supposed to be the same size as the pads!! Typical PCB manufacturer recommendations are to reduce the apertures about 15% (by area). For hand stenciling, you might even want to reduce it a bit more.
On the most recent PCB I did, in Altium, I set to -15% as the global paste mask reduction setting, and for large ones like thermal pads, around -20%. Then I went through every damned footprint and reviewed the paste mask reduction for all the pads, because it turns out that many footprints are set up to override the global setting and use 0% reduction instead.

The result was hands-down the best results I’ve had with a stencil. Not a single short, not a single incomplete joint. On the smallest components (0603) it could probably have even gone with -20%.