The solution to that is to lower the speed of your tankers a bit so when they arrive theres enough fuel for them.
As above, Sorium harvesters on ships using default commands look for the highest acc rating. This leaves one of two options, if you still want a fire and forget ship then you need to SM and alter the ratings, so your first choice is highest. Second option as has been discussed is to use a static station/ship and shuttle the fuel. the only way to avoid then interrupts due to a lack of fuel on the station is to set the shuttles with a very low speed amount. Anything else from these will give you interrupts of one form or another.
I believe the default unload 90% order also picks the nearest colony to the sorium source at the time of the tanks being full so this has potential for many problems also. I generally do my fuel harvesting one of two ways.
1. A station in orbit doing the harvesting of sorium with huge tanks for storage. Small slow shuttles that take the fuel to a fuel dump colony (always the innermost moon of the gas giant). Finally fuel tankers that come from various points in the empire to collect fuel and unload back at their respective home bases (on an endless cycle order)
2. A station in orbit as per above. Fuel tankers that operate as above but this time refuel directly from the station and remove the fuel dump moon colony, again on endless cycle orders.
Both methods work well enough, both involve some working out speed settings of ships to ensure there is always plenty of fuel left in the station tanks or colony dump stores. I tend to start with #1 then switch to #2 when I start spanning multiple systems and want fuel to move faster around as I will have multiple versions of #2 set up.