In the transition to 3DS, Grezzo took some liberty to change a few things around. This page is meant to cover the more meaningful changes instead of the minor ones like text changes, unless the change adds considerable value with the new text somehow.

In the original Ocarina of Time, you could – if you were fast enough – re-bottle one of the three bugs when you dump them onto a soil patch to get the Golden Skulltula token. Using the trick allows the player to only need to catch one bug in order to get the Skulltula tokens in the soil patches. It cannot be done in the 3DS remake, sadly.

This includes soil patches that have already had their Golden Skulltula token collected. In other words, you need to be careful when playing the 3DS version. A good way to avoid this problem is to keep a checklist of the 10 Magic Bean soil patches, or don't collect the tokens until it's time to plant the bean. Then you'll have the sprout as visual proof that you've collected the token and won't need a checklist. :)