It may be a rooted cutting and not grafted. It's hard to tell from the photo. If rooted cutting, then everything you see is pure lime.

Crushed lime leaves usually have a limey aroma, so that's one way to check. If all the leaves smell/taste the same, then you're good. It's just a matter then of what shape or form you want your plant to take on.

Thank you. Yes they smell very limey. What would you recommend? I feel I looks kinda weird and I just want it To have a clean look to it

It is very likely that you have rooted cuttings and two of them. It may be possible that the second plant is actually attached to the other one below the soil. But bet they are independent plants. You can separate them into two plants. The roots will be tangled and so it would be a bit time consuming process to separate them. Since the plants are young it will be easier now - the more you wait more they will be tangled.

If you want one upright trunk, then cut away everything else coming out of the ground, or low off the trunk. It would certainly set it back a year or so. Your call really. It's fine as a bush.

Limes are bushy little things. This looks normal. Looks like a cutting the way the branches come out of the ground. It's cute! Let it grow.