There are no Upwork user interface buttons or settings that will allow you to force an hourly contract to pay at least one hour's worth.
So your two main options are:
a) Don't worry about this. Decide that the number of jobs you do which actually involve less than one hour's worth of work are not worth doing anything about this issue.
b) Do something proactively on your own about this, by stipulating something about this with clients before accepting contracts.
If you decide to use option (b), then you could stipulate to a client - before she hires you - that you require all contracts to allow manual time, and you can stipulate that if a job takes less than one hour, that you will add additional time using manual time in order to make the total time equal one hour.
(The client would still be able to dispute manual time and have it removed from the time she pays you, but you would trust that she would not do that.)
Alternatively, you can stipulate to the client - before accepting the contract - that she will need to use the client-side Pay Bonus tool to pay you an amount of money necessary so that you are paid for a full hour's worth of time.
(And you understand that the client would be on the honor system to actually do so.)
When a potential client tells me they think they'll need no more than an hour (or two) of my time I tell them that will need to be under a fixed price contract, not hourly. We agree before the contract begins what exactly they will need from me.
Trusting that an unknown client will actually pay me for manual time, which they can easily avoid paying, is a luxury I don't want to pay for with unpaid work time.Not even for an hour's work.
I am very transparent with them. I tell them we will stick to a specific maximum time limit or less of my time and, if it becomes necessary that I work beyond the time allotted in the first milestone, they'll need to set up and fully fund a new milestone for the additional work and time.
I have never had a client need to set up an additional milestone. I do my best to see they get what they need from me under the first milestone.