My 2c: Its a low production Fender. Even in the Leo days, they were typically not all perfect. This kind of cosmetic thing neither affects the appearance to the fans at the gigs nor to other musicians. No one is going to look that close. I would personally forget about it and play it. A lot. Its a fantastic bass.
OK, that said; if you want to undertake mods (which this would be), then do it the right way. In that case, wood filler or toothpicks are not a great idea, IME. The proper "fix" is a really small diameter hardwood dowel, properly installed followed by correct touch up with a nitro paint. Best done by a luthier with nitro finish experience to get it right.
Sorry this bugs you. I would personally just take it as part of the bass's personality and play on. GL