runner has to avoid running into shortstop when fielding the ball - if the pitcher or 3rd baseman hadn't missed the ball first
Even if the ball had already passed another fielder- for instance, with F5 playing in and F6 back behind her- if the shortstop has a legitimate opportunity to field the ball she is also protected from interference.
Once the ball has passed another fielder, the runner can be absolved of interference with the
ball if it hits her in some cases, but she is not absolved of interference with a
fielder who might still have a play.
If two fielders are going for the ball in the same vicinity (at the same time, at the same depth, in the same area) only one gets protection from interference- the one that, in the umpire's judgment, has the most reasonable chance to field the ball.
On the original post/question: Interference is a good call. When it comes to fielding a batted ball, fielders have the absolute right-of-way. Runners must not interfere, either intentionally or accidentally.