Had a look at one of my hives today and it has a large split in the wood below. Nothing hit it, but we have had a shift in weather going into March. It is on the other side as well just smaller. Only happened today as I did not see it yesterday.
Will this be an issue?
Could I fill it with something?
You can fill it with some silicone or PU based caulk. It will be pushed out when the timber will start to move the other way. Bees will propolise it from inside.
If you have a spare box and some woodworking equipment you can fix it better.
In general, it is worth sanding timber before coating to have a less open grain.
Please bear in mind that I am no carpenter, but as that crack crosses the handle, I would be inclined to screw in some flat plates across it, bridging the gap. My reasoning is that the weight of the whole box will be carried only by that one tongue interleaving at the corner. I would not want to risk the box falling apart as I lifted it, especially if it was full. 
I was going to try and fill it with wood glue, woud that work?
just bought another hive, we be a hassle to buy a new box as well
If you are talking about PVA, it is not a particularly good filler. It has a lot of water in it - 50% and more. When water evaporates, PVA forms a film. You can make a PVA-based filler by mixing it with something like wood dust or cement or gypsum. Another problem, it is water-resistant glue. Not waterproof. Even “exterior” PVAs product data sheets usually say something like “exterior applications which are not exposed to weather factors”.
If you are hoping that PVA is going to hold things together, it will not. PVA requires well-fitting surfaces to work well.
If you don’t want to spend money and have soil with high clay content, you can do what beekeepers were doing as a temporary fix for ages. Grab some dirt, fill the crack and forget about it till you can really fix it 
If i needed to use wood glue for any reason, on outdoor wood, I would use Titebond 3. 
Wood glue is for sissies. Epoxy and fibreglass!
good to know. It is the broodbox, so it won’t be lifted or moved much, I just don’t want the crack to get bigger/ more cracks really! I do have some caulk which might be better by the sounds of your other message
It looks to me like two different boards were butt joined & the join has opened up. As long as the crack is dry, you can fill it with Plastibond. If you want, you can also make same joiners from strapping & put one on each side of the handle, using 1/2" galvanized button head screws, like in my photo. These are all available from Bunnings.
I would also consider putting a screw in each of the dovetails.
cheers
