These are the kind of questions that keep me awake at night. Not. Just kind interesting though.
WotC didn't give away the rust monster, that's still their intellectual property. They did include it in the d20 System Reference Document, which means that anyone releasing products under the OGL can make use of rust monsters in their work, but
only if they do so according to the licence provided by WotC.
You aren't misremembering the history of the rust monster as a toy. I recommend Tony DiTerlizzi's
article on this topic for some great pictures. Whatever intellectual property might be associated with the original plastic model still belongs to the company (or companies) which manufactured or produced those toys. But there is more to the Dungeons & Dragons rust monster than just its appearance; the D&D version has a name and special abilities that make it a "rust monster", rather than simply a prehistoric creature that looks exactly like a rust monster.
Given that (and the amount of time that has passed) it would be difficult to build any kind of legal case that TSR and WotC infringed or are infringing any of the original toy producers rights. It's also perhaps notable that these toys were originally marketed as "prehistoric animals", so presumably they are supposed to resemble actual historical creatures, and nobody can claim exclusive rights to the shapes of real creatures.
If you are looking for something to ponder while you deal with insomnia, a more interesting edge case is probably the displacer beast. That's a creature not included in the d20 SRD, so its use is restricted to WotC (and any licensees not relying only on the OGL). However, the displacer beast is heavily inspired by the coeurl, a creature created by A. E. van Vogt in a 1939 short story titled
Black Destroyer, so while WotC can claim to own the "displacer beast", they don't have exclusive rights to publish a creature which looks exactly like a displacer beast/coeurl.
It delights me more than it probably should that Paizo actually went to the trouble of getting permission from Van Vogt's estate so that they could include a coeurl in
The End of Eternity (the 22nd Adventure Path release). Wes Schneider wrote a great article on this subject
here.
Come to think of it, both the displacer beast and rust monster would be interesting creatures for the
Monster ENCyclopedia series (eventually).