(1) There is fear that any advance in nuclear power technology will lead to corresponding advances in nuclear weapons technology. For instance, if somebody built a perfect system for separating out protactinium from a thorium MSR, that protactinium could be allowed to decay outside the reactor and produce pure U233 that could be used to make weapons. That perfect system is probably not practical, but in general there is fear that any new approach to fuel processing could have unintended consequences. Would it be possible, for instance, to make something like the EBR-II that breeds weapon grade plutonium in a blanket and uses some form of pyroprocessing to produce pure metallic plutonium? Such a system might be able to make enough material to build several weapons a year.
(2) The published information about nuclear proliferation is incomplete and the mental models behind it are broken. For instance, the "little boy" bomb was made with uranium produced with a
https://en.wikipedia.org/wiki/Calutron
but for all the fear that countries like Iran would develop centrifuges, there has been little fear expressed about Calutrons... Except that when Iraq tried to develop a bomb it used the exact same approach used by the US! A scientist at CERN had been contacted by an Iraqi scientist who was interested in a magnet which could have been used for a Calutron and the proliferation authorities just blew him off.
See https://nuclearweaponarchive.org/Iraq/andre/ISRI-95-03.pdf
A country like Japan has large amounts of plutonium which is contaminated with Pu240 and Pu241 and not weapons usable but it's plausible that a modified Calutron could be used to purify non-weapons grade plutonium and make it weapons grade.
Although the conventional model is that a threat would make plutonium by irradiating uranium with neutrons from a fission reactor, it's also possible that a fusion reactor or particle accelerator could be used as a neutron source to do the same. The later would actually have less heat output per unit of Pu and might be an easier device to hide. Current particle accelerators aren't reliable or economical enough for this purpose, but this is just one of many paths to proliferation which are ignored.