Some applications open in low resolution
Retina must be supported by the app for it to be displayed in Retina. If the app does not support Retina then the app will not be displayed in Retina.
You may be able to force Retina for an app with Retinizer:
Retinizer is a small app I wrote that allows apps that aren’t retina ready and are displayed pixelated at 1x to display their UI widgets at 2x. That way, only their custom images will look bad and not the whole app.