Embedded media loses alignment classes

When I have the Limit allowed HTML tags and correct faulty HTML filter after the Resize media images and Embed Media filter, the embedded media item loses all of the regular entity markup. If I place the Limit allowed HTML tags and correct faulty HTML filter before the others, I get the markup back, but the only class on the <article> tag is media-embed-resized, all other classes are lost, so for example no alignment classes etc.