If you check your Scanner in the City mode, you should see your ship highlighted in Green.
Go to the position and click the Enter link.
Your ship should be one of the options.
Enter the ship, then enter the cockpit.
I find refreshing your browser helps as you seem to re-load a previos page rather than refresh automatically.
Still new to the game, hope this is correct and helps.
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The truth is a 3-edged sword:
Your Side, Their Side and The Truth