In the OPs situation - no problem, batsmen's own fault.
In the Elliot/Sidebottom situation - correct decision made. It was a 'racing incident'. Sidebottom was fully entitled to take that line to get the ball and made no wilful attempt to impede the batsman. An interesting point, however, is the running line taken by Elliot. In good Club cricket (which I umpire) the batsman almost always runs down the opposite side of the pitch to the non striker (to avoid possible collisions) - this should be even more common practice higher up the game. However, it is a neat trick used by some batsman to drop the ball close to the bat and take a line to 'run the bowler off' - I would suggest Elliott was doing this. Certain subtle recent changes to the Obstructing the Field Law might cause a question for an umpire in this situation
In the Bell situation - although technically under the Laws it was a run out the fact that many of the Indian players clearly thought there was no further action on the delivery and, perhaps more importantly, the bowlers end umpire was giving the sweater back to the bowler (although they might take it of their own accord I would not offer it until I was content that all worthwhile action on the delivery was complete) indicates that, possibly, the strikers umpire, might have decided differently. Ironically the day before this happened I had a moment in the match I was umpiring. A single had been taken, the cover fielder chased down the ball and, as there was no serious thought on either side regarding a 2nd run, he threw the ball to mid off the batsman at my (the bowler's) end decided to do a little gardening. Mid off shaped to throw at the stumps and looked at me. I shook my head. Although technically under the Law the ball wasn't dead in all common sense it was - and the fielder fully accepted this.
In the Murali situation the problem was Murali set off very quickly to congratulate the batsman. The fielder could reasonably have thought a run was being attempted. Had Murali waited even a couple of seconds I suspect the umpire may have disallowed the appeal.