In the opening credits, the S.S. Minnow that is shown before the cruise, and after beaching on the island is different of the one shown during the storm. (No upper deck above the windows where the helm is, and the front of the cabin is straight, rather than pointed.)
Occasionally the radio announcer would announce the call sign of the radio station the castaways were listening to, and it would always start with W. With few exceptions (and even those don't go any further west than Texas), radio stations with call signs that start with W are east of the Mississippi River. The castaways were somewhere in the South Pacific and had only an AM radio, and even in the most perfect conditions, it would be highly unlikely the strongest AM radio station east of the Mississippi could have reached them.
On a number of occasions, the castaways encounter people, whether other castaways or fugitives in hiding, who have been on the island for 10 years or more, prior to the arrival of the Minnow. All these characters regard themselves each as being the only person on the island. How big is this island that all these people could exist there so long and never know about each other?
It has often been observed that although they were on "a three hour tour," the castaways have an awful lot of supplies. Mary Ann and Ginger have seemingly not ever worn the same clothes twice, the Professor has an extensively library, the Howells have myriad luxury items, etcetera.
The Skipper breaks the fourth wall on numerous occasions. One might argue that this was intentional and done for comedic effect, but oftentimes it happens so quickly that comedic effect doesn't have time to take hold. It appears to be done to show the Skipper's frustration with Gilligan, but at times, it seems to be a case of the actor appealing to the director out of frustration.