When it comes to body filler there are lots of factors to consider. for plugging a hole, even a tiny one, it's probably the wrong product as body filler has no structural strength. The suggestions of JB KWIK or just about any epoxy are better choices.
This kinda goes off on a tangent, so feel free to tune out.
The comment on cracking Bondo got me thinking, though so I thought I'd offer my 2 cents. I haven't been in the field for 10 years, so I'm sure there is new product out there, but do have several years experience in auto body work, and am familiar with the basic products used... and the ways they are often mis-used. When it comes to something as small as an O gauge train, even medium build body filler such as bondo seems like it would be of limited use.
In auto-body a product such as Dura-glass is used for large, rough-in repairs in combination with fiberglass sheeting. almost never the actually correct way to fix the damage, but it's cheap and gets the job done. In most cases medium weight body filler is used next. For cars this product works great. but on trains? I think it would still be too rough. This is a product like Bondo, though the actual brand name Bondo is not very good and prone to cracking. At the shop I worked we used Evercoat brand products, and can not recall ever having problems with cracking. All body fillers can crack or shrink, though, and this is often cause by adding too much hardener when mixing. When it comes to detail, you can only sand this stuff down to about 120 grit, after that it won't get any smoother and we typically finished there with 80 grit.
When it comes to filling on a model train I think the next step down would be the most useful. A body glaze filler is used to fill small scratches and rock chips. this stuff works just like a bondo product, but is much thinner. the stuff we used would sand nicely to 240, or finer. I think Body glaze is gonna be the product you want for 'body work' on your model trains. Your JB Weld will behave much like a body glaze, but dry much harder. Good for replacing metal parts, not so much for fine detail sanding. The glaze is also cured to a sand-able level in 5-10 minutes.
The last bit that many people don't tend to realized is part of the actual body work is the primer. A good primer will fill small imperfections, and most importantly it fills the scratches from sanding body filler. wet sanding primer with 400-600 grip paper provides a nice smooth finish.
TLDR: Bondo (medium build body filler) is probably too coarse of a product to use for models. try the next step up and use body glaze, and don't count on body filler to plug holes, it doesn't provide structure. sort of like filling a hole in a wall by spreading mud over it. works fine until someone pushes on it.
JGL