Yes, but maybe it's an error.
The description of the spell as written does indeed say that if the indigo layer starts to, but does not succeed in, petrifying a creature, then prismatic wall ends.
But given that the other language in the spell description strongly implies that that the only way to end the spell is by successively bringing down each of the seven layers, that seems really incongruous.
So, here's a theory. Suppose that in an earlier draft of the spell, the indigo layer's effects read something like this:
6. Indigo. The creature is subjected to the effects of the flesh to stone spell.
At some point, someone realizes that flesh to stone requires a Constitution save, which is inconsistent with the other Dexterity saves that the wall requires. So the indigo layer's effects are spelled out by copy-pasting in text from flesh to stone:
A creature restrained by this spell must make another Constitution saving throw at the end of each of its turns. If it successfully saves against this spell three times, the spell ends. If it fails its saves three times, it is turned
to stone and subjected to the petrified condition for the duration. The successes and failures don’t need to be consecutive; keep track of both until the target collects three of a kind.
This is nearly identical to the printed effects of the indigo layer of prismatic wall, in particular the contentious the spell ends wording.
I suspect that instead of the the spell ends, what is meant here is the creature is no longer restrained. Because there actually isn't any phrase the description of prismatic wall that specifies how long the affected creature is restrained for. Compare to other spells which impose the restrained condition:
The target is restrained until the spell ends,
On a failed save, the creature is restrained as long as it remains in the webs or until it breaks free.
And, indeed, prismatic wall already imposes another condition, and it specifies a duration for that:
If another creature that can see the wall moves to within 20 feet of it or starts its turn there, the creature must succeed on a Constitution saving throw or become blinded for 1 minute.
But the most compelling reason to think that the spell ends is a copy/paste error is the text for the related spell prismatic spray. The effects for the indigo ray of that spell use the same language:
6. Indigo. On a failed save, the target is restrained. It must then make a Constitution saving throw at the end of each of its turns. If it successfully saves three times, the spell ends.
But prismatic spray has a duration of Instantaneous; it's already ended by the time the target is making a third saving throw. The phrase the spell ends has no real meaning in the context of an instantaneous spell.
So, my contention is that the intent of the effects for prismatic wall is that saving three times against the effects of the indigo layer means that the restrained condition on the creature is ended, but the prismatic wall is not dispelled.