There were several things in the flexbox spec where Chrome refused to implement what everyone else was doing and the spec ended up getting changed, but I don't have links offhand, sorry. It would take me some hours of digging through bug reports and mailing lists to find them. In general, there have been a lot of things like this in the CSS world that I see peripherally, but I'm not as involved in that personally, so don't have them at the tips of my fingers.
A recent thing that came up is that the behavior of the `disabled` property on `HTMLLinkElement` in Chrome does not match the (very long-standing; literally decades) spec, and it looks like at this point we're going to need to change the spec to match Chrome because sites are writing code to the Chrome implementation, not to the spec, and it's causing compat problems for Firefox (which does implement the spec).
Now don't get me wrong: there are lots of cases in which Chrome _does_ fix longstanding spec-compliance issues. But that's not the only dynamic happening here.
For the rest, I work on Gecko (the rendering engine in Firefox). We get a fair number of bug reports about sites that work in Chrome but break in Firefox because Firefox is following the spec and Chrome is not.
Chrome is definitely closer to the standards than IE was, but that's at least in part because of all the changes standards have been making recently to match Chrome when Chrome makes it clear that they have no plans to implement what the standard says. When IE tried that sort of thing, people just wrote standards that didn't match implementation reality. That had its own drawbacks in terms of leading to standards so divorced from reality they were useless (see XHTML 2.0, for example)....