You are correct in saying its a CSS issue. The token-input-dropdown box has its position set to absolute. This introduces layering.
Its parent element, the ui-dialog box is also set to position absolute. It has a z-index set of 1010. Your token-input-dropdown has a z-index of 1 which means it will always be underneath the ui-dialog. Modify the CSS to set a z-index greater than 1010 on your token-input-dropdown.