You may have clicked "Yes" when VS asked you if it should run the last successful build when compilation fails.
See here for how to change the setting.
There are plenty of issues like this with F# in Visual Studio, but the situation also improves all the time in VS 2017. I believe one possible workaround for this particular issue is to restart VS.
But there is also another way, which works better to avoid an inconsistent Error list pane in general. Change from "Build + Intellisense" to just "Build" in the dropdown in the Error list pane, and see how that works for you. It means you have to compile to refresh the Error list pane, but you still get (sometimes inconsistent) Intellisense help in the editor panes without having to recompile.
If you want to know more about F# issues in VS, this is where to look: https://github.com/Microsoft/visualfsharp
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