3) has been noted here before. It's clear from the way his coat blows about that he couldn't possibly be carrying the bottle. Maybe he nicked it on another occasion and was just using that as a cover story.
More than any of these though, we're asked to believe that the victim suffocated in a large room, clearly not airtight, simply by an air conditioning unit being switched off.
I've always felt that "Any Old Port" is strong on character development, but, yes, a little hard to swallow sometimes. There are quite a few other episodes I believe have some far-fetched aspects, too, although with most the overall quality certainly isn't diminished because of those aspects.
Also regarding #3, I think somebody once noted that if the wine room were truly air tight, the outside temperature would not have any effect on the temperature inside the wine room.
One other thing that's been mentioned before is the wild weather swing. One day was chilly and rainy (I think Columbo actually said in the 40s) and then within a day or two, the temperature soared to over 100.
I couldn't get by the first and second points, let alone the fact that rigor mortis would have made the stinky task just about impossible, but if we were to nitpick over every flaw in these productions, there would be no way to enjoy the show. There's nothing wrong in pointing them out for the sake of forum discussion, but I think we can all agree that every episode sports inconsistencies from reality.