As far as the print this can be solved by increasing the infill density and/or adding more top layers. Also the type of infill will have an effect on this.
On the fan, do you mean the left one of the two that are on the front? Normally these are set to run once the temp reaches ~50c.
To supplement the answer given by whirlybird.....
By default, the makerbot dual extruder has three fans....one fan on each of the extruders to stop the feed side of the extruder from heating up (and melting the filament before it gets into the head!), and one user controllable cooling fan.
The two extruder cooling fans...the ones facing the front of the printer, ,,will run whenever the relevant extruder head is above 50 degrees C. They'll start early on in the warming stage, and remain running after the print has finished until the head temperature falls below 50 C.
The third fan...the one fixed to the LHS of the head assembly, is the fan the slicer has control over...and is controlled from the Cooling tab in settings.
I have seen an add-on available for the 2X that is a mount and duct for a second cooling fan that plays directly onto the print at the right hand extruder nozzle. I have no experience of this...or as to whether it can be controlled separately to the LHS cooling fan.
And regarding the printing issue, I concur with the answer given.