I don't get the whole Grey Matter open ended thing so many people gripe about. IMO it is pretty clear what happened.
S1E5: Walt and Skyler visit Gretchen and Elliott after many years. G&E had every reason to be awkward about Walt leaving the company but they were gracious with them. Elliot even reminisced fondly over Walt's present about their college days. Elliot then offers Walt a job which could provide health insurance, a higher salary, and get Walt back on the right career track in the science field. Walt rejects this to continue making meth, an illegal substance, where other than money provides no benefits for his family. Vince Gilligan himself admits THIS is where Walt breaks bad, not because of cooking meth but when provided with his first "out" he refuses to take it.
S2E6: Walt lies to Skyler that G&E are paying for his health insurance when it is his meth dealings that do so. Skyler, suspicious about Walt's disappearances yet grateful for G&E looking out for Walt, thanks Gretchen for being so kind. Gretchen's like
and tells her that they never paid for it. Gretchen invites Walt to dinner to ask why he would refuse their offer (even after lying Gretchen's still willing to pay for it) yet lie to his wife and say they are. Walt went off on what he perceived as them cutting him out while Gretchen counters by bringing up the dinner at her father's house where Walt saw how rich they were packed his bags, left, dumped her and sold his Gray Matter shares BEFORE they succeded. Note that Walt never denied Gretchen's account of what happened but continues to ignore her and call her names like "little rich girl".
Walt sold his ownership of the company he helped found and they blew up later on. I don't see how this was ever Gretchen and Elliot's fault.