While no cannon explanation is offered, one can infer that the reason lies in the primitive, and utilitarian nature of the Destiny Gate System, as opposed to the Destiny's gate itself and the newer Milky Way and Pegasus gate systems.
It is likely that as time progressed, the Ancients refined their manufacturing techniques, equipment, and gained experience and understanding with their original stargate network (of which the Destiny Gate System is likely based upon) they had eliminated the issue altogether.
NOTE: Keep in mind that Ancients implemented strict controls, which were "built into" the stargate network protocols, thereby
preventing such situations as time travel through wormholes on typical
travels through a stargate.