1.) Why is this happening?
Could be lots of reasons. Perhaps your efficiency is different from that assumed by the recipe or recipe calculator. Maybe your water chemistry/pH is also effecting it. Maybe your grain crush is a little off. Maybe your hydrometer/refractometer is slightly off. Etc. Etc.
2.) How do I fix it?
Need to know more info about your recipe source and process, honestly.
3.) Does it matter?
That's probably more a function of the finished product. If your FG comes in at roughly the same delta under target, then you can start to suspect your measuring equipment or readings. How does it taste? If it tastes good, RDWHAHB.
4.) At what point is the delta negligible? 0.001? 0.002? 0.010?
Probably a function of the taste and strength of the beer. If you got 1.101 when your target was 1.105, you might not notice.