You seem to be certain of your facts , otherwise  as in the cases of large tiles, were it might say 1 million resources, but its a million +a few k,I might have suggested your situation might be because of 'rounding.'

That is, it might say it will take an hour to finish yielding but its actually over one hour by an unknown amounts of minutes, so putting  on a 1 hr domain guard isn't going to help.

I appreciate that we would all like to get the maximum usage ,but from personal experience, its better to wait till the time says less than an hour before applying the shield,rather than trusting the times are accurate,or just send enough troops so that you already know the time will be less than 1 hr.