Many Cuneiform signs are structured as a container sign with a second sign infixed (occasionally more than one infixed). Quite a number of these show alternations with signs which are otherwise identical, but which have the "infixed" sign components outside the "container". Here are a number of examples.

Gary Beckman has pointed to one example from Hittite. The Hittite sign SI x SA2 (= SI x DI) with infixed DI is equivalent in form and meaning to the Mesopotamian compound SI.SA2 (= SI.DI) where the DI is external to the SI.

Within Mesopotamian Cuneiform, there are a number of cases of such alternation.

Looked at through time, there are a number of signs which "push out" the infixed sign so that later forms have it externally. The first examples here are those where the infixed component is also itself an independent sign.

HI x BAD (Labat #406, Fara #366) has BAD inside HI earlier, later HI.BAD

HI x ASH (Labat #405, Fara #361) has ASH inside HI throughout, but a late distinction with HI.ASH (historically related ??)

GA2 x GI4 (GAGIA Labat #256, Fara #681) has a later form shown in the Fara list GA2.GI4.

DUG x KAK (DUR Labat #108, Fara #549) has a later form DUG.KAK.

Some such examples may be simply the graphological change of parts of signs which are not themselves independent signs. The first four here all show the same pattern, gunation within the body of the sign in early forms being lost there and appearing following the main body of the sign in later forms.

DUG.gunu (USAN, Labat #107, Fara #556) has the crossing lines called "gunu" external in later forms, the base sign preceding that is the same that results from DUG without the lines called "gunu". The "gunu" is not an independent sign.

HUR, HAR 'ring' (Labat #402, Fara #370)

KUN 'tail' (Labat #77, Fara #754) has "gunu" in the main body of its sign early, but these appear instead outside of the main body of the sign in later versions, with the main body reflecting a form without the "gunu".

AH, UH 'insect, parasite' (Labat #398a, Fara #367) has its internal crossing lines external in later signs. (And A' Labat #397 is a sign distinct from AH only in later forms.)

BIR 'kidney, testicles' (Labat #400, Fara #372) has its internal parts appearing external in late and Assyrian forms.

SIG7 'bright, clear' in its earlier forms shows several parallel lines superimposed on a base IGI. In later forms, these lines come to be external, to the left of the base sign.

When SIG7 is infixed within a rectangle, in the sign AGAR2 (LAGAB x SIG7) Labat #500, we see that first process, and then a similar process again later in which the parallel lines move outside the rectangle, to precede it also.

Contrast between two signs differing in this way seems to be at least rare. The only example I have noticed so far is Labat #579b A.IGI which occurs in a use for 'tears, lamentation' vs. Labat #581 A x IGI which occurs in a use 'to cry'. These meanings are very close, so this is not a clear case of contrast.