Riccardo is correct, GHC doesn't infer that your guards can't possibly all be false. So accept his answer please.
I'm going to digress and talk about coding style.
Your motivation for not using otherwise may have been that it looks unsightly:
insert :: (Ord a) => a -> Tree a -> Tree a
insert x EmptyTree = Node x EmptyTree EmptyTree
insert x (Node a left right)
| x == a = Node a left right
| x < a = Node a (insert x left) right
| otherwise = Node a left (insert x right)
Looking at this code, a human reader must confirm to themselves that the final guard accepts precisely those cases where x > a.
We could instead write it like this:
insert :: (Ord a) => a -> Tree a -> Tree a
insert x EmptyTree = Node x EmptyTree EmptyTree
insert x (Node a left right) = case x `compare` a of
EQ -> Node a left right
LT -> Node a (insert x left) right
GT -> Node a left (insert x right)
The Ordering type returned by compare has only the three values EQ, LT, and GT, so GHC can confirm that you've covered all possibilities, and a human reader can easily see that you've covered them correctly.
This is also more efficient code: we call compare once, instead of calling == and then probably calling < as well.
Now I'm going to digress some more and talk about laziness.
You've probably also written a function similar to this:
contains :: (Ord a) => a -> Tree a -> Bool
contains _ EmptyTree = False
contains x (Node a left right) = case x `compare` a of
EQ -> True
...
When x == a, you need to know that the tree uses the Node constructor, and that its first argument is equal to x. You don't need to know what either of the subtrees are.
But now look back at my definition of insert above. When the tree it's given is a Node, it always returns a Node whose first argument is always a. But it doesn't state that up front: instead it evaluates x `compare` a.
We can rewrite insert to perform the comparison as late as possible:
insert :: (Ord a) => a -> Tree a -> Tree a
insert x EmptyTree = Node x EmptyTree EmptyTree
insert x (Node a left right) = Node a newLeft newRight
where comparison = x `compare` a
newLeft = if comparison == LT then insert x left else left
newRight = if comparison == GT then insert x right else right
Now we return the Node a bit as soon as possible --- even if the comparison throws an error! --- and we still perform the comparison once at most.