The problem is that many of these accounts rely on eyewitness evidence which is notoriously unreliable. And even if the witness is trustworthy, he usually can't reproduce what happened -- not his fault, of course, as this is the nature of these sorts of things. I think I get Deja vu quite a lot of the time, but it might just be two things that are similar matching up for whatever reason.
Not everything can be explained, not yet at least, but the general trend is that the weird paranormal stuff turns out to have perfectly rational explanations. I see no reason why this won't continue, and that yet more apparent paranormal events will turn out to have been random effects, or people seeing things that weren't there, and so on.
As to the case of your sister seeing her Dad's army number on the glass, without being there I can't possibly comment. How did the glass get there, whose was it, who put the number on the glass and so on? I can't blame you for feeling uncomfortable about it as these incidents do tend to defy explanations at least initially.