By default Mailspring draws its own window frame and title bar so they can follow the Mailspring theme (dark in dark mode, and so on). If you'd rather have the window controls and menu bar come from your desktop environment so they match your GTK theme, open Preferences > Appearance and change Window Controls and Menus:

• Default Window Controls and Menubar — your desktop's title bar and an always-visible menu bar. Pick this if you see two sets of window buttons (common on GNOME and COSMIC).
• Default Window Controls and Auto-hiding Menubar — the same, but the menu bar only appears when you press Alt.
• Custom Window Frame and Right-hand Menu — Mailspring's themed frame with the menu behind a button in the top right (the default).

Click Relaunch when prompted for the change to take effect.