Near as I can tell this only happens if the ships are in que going to different towns.. when using a single target town it seems to recalculate correctly.
Scenario, was sending out freighters, but also had a load of cargo's.. I realized they was last in line and canceled teh freighters which should have reduce the cargo's loading time from 1hr 15mins down to about 7 mins.
it didn't.. see pictures 1 2 3
I was able to repeat this bug several times without fail.