Currently a lot of extensions will conditionally load modules based on the content of the page, e.g. only load math code if equations are present, or only load MultimediaViewer if images are present.
When VE is used the content of the page will change asynchronously, and these modules will not be present if an equation or image is added, for example. In some cases (e.g. math) the module is actually loaded by VE, so the problem is bypassed, but others (e.g. MMV) aren't required in VE, but are required after save.
Ideally we could run the same content-checking hooks asynchronously and load any modules that are required automatically.