There are only two Zelda games I have this problem with: Majora's Mask and Twilight Princess. It's always specific dungeons I get into and just stop at.
In MM it's Snowhead Temple, it's not a bad dungeon, I just don't care much for it. When I get there it feels really meh to me, like I'm just going through motions to get to other parts of the game I like better. As a result, I usually end up losing my interest because I'm longing to get to Great Bay and eventually Ikana, and that longing to be at other parts of the game makes Snowhead such a slog for me. I usually put the game down for a month or two, the way I get back into it is hyping myself up for my fave part the Snowhead region offers: the Goron Race. I can only do the race by making it Spring which is why completing Snowhead Temple will be worth my time. Once I make it Spring and win the race for the Gold Dust, I can upgrade to the Gilded Sword, so that is another driving factor to get me through Snowhead Temple.
In Twilight Princess I lose all steam in Snowpeak Ruins. Yeah... I guess if it has snow in the title it's bound to be my mental hurdle point to keep playing. I stop at Snowpeak Ruins for the complete opposite reason that I stop in Snowhead Temple for. I actually like Snowpeak Ruins but for some reason it's when I get there that my mind decides to make me hyper aware that City in the Sky is getting close. Technically I still have the Temple of Time ahead of me first, another dungeon I like, but I feel like if I progress past Snowpeak, City in the Sky is just looming closer and closer.
The longest I've put off TP because of that is 2 years. To get myself back into it I do something similar to what
@Fraxinus brought up. I start roaming around to areas in TP I like a lot, I usually go fish at the fishing hole a lot too. Then I tackle Snowpeak Ruins, Temple of Time, and once I'm at City in the Sky I just push through because I really want to get to the Palace of Twilight, and I start reminding myself that I actually do like the boss battle with Argorok.