Looks like you've accidentaly assigned a value to Derivative:
(* How the y''[x] expression looks without nice syntax: *)
y''[x]//FullForm
(* Derivative[2][y][x] *)
DSolve[{y''[x] == y[x]}, y[x], x]
(* {{y[x] -> E^x C[1] + E^-x C[2]}} *)
y''[x] = whoops
D[y[x], {x, 2}]
(* whoops *)
whoops = y[x]
D[y[x], {x,2}]
(* y[x] *)
(* Let's try to fix it by clearing y *)
ClearAll[y];
D[y[x], {x,2}]
(* y[x] didn't work *)
(* Clear the strange definition by: *)
y''[x]=.
D[y[x], {x,2}]
(* y''[x] *)
What goes wrong is the assignment to y'' which is easier to understand by remembering the FullForm:
Derivative[2][y][x] = something
making all kinds of strange things happen.
