If one is attempting to get to the apex there is a possibility of error wherease if one's intention is to prepare short, it matters very little just HOW short.
If a canal is curved bucco-lingually and many are, and if the radiograph is taken bucco-lingually which most are, then if the tip of the probing file is short of the apex, the distortion caused by the curve can make it difficult to know where the tip of the file is relative to the apex.
And this is particularly true of a filling.
If there is a puff of cement beyond the apex, there is little doubt that the rest of the canal is filled, especially in a cement filling since puffs cannot occur INSIDE the canal.
The idea is that with rare exceptions, if there one canal is filled to the apex, the other canal will be sealed off from apical tissues as well.
If, on the other hand, one fills short it may be short of the junction of the two canals and thus exposes the entire unprepared unfilled canal to the apical tissues.
In cases where the canal is completely sealed, any problems are usually caused by trauma, which are while the patient is still under treatment and can be handled with analgesics and occasionally with antibiotics.
Problems that occur with underfills are usually infectious processes and can only be solved by retreatment, frequently after months or years have gone by and after a restoration or post has been cemented.