Fix the order of _free_encoder_inputs (#38907)

Signed-off-by: Tianyu Guo <guoty9@mail2.sysu.edu.cn>
Co-authored-by: mergify[bot] <37929162+mergify[bot]@users.noreply.github.com>

vllm/v1/core/sched/scheduler.py

@@ -996,14 +996,6 @@ class Scheduler(SchedulerInterface):
                 request.use_structured_output and not request.is_prefill_chunk
             )
 
-            # NOTE: _free_encoder_inputs relies on num_computed_tokens, which
-            # may be updated again in _update_from_output for speculative
-            # decoding. However, it is safe to call the method here because
-            # encoder inputs are always part of the prompt, not the output,
-            # and thus are unaffected by speculative decoding.
-            if request.has_encoder_inputs:
-                self._free_encoder_inputs(request)
-
         # Clear the finished request IDs.
         # NOTE: We shouldn't do self.finished_req_ids.clear() here because
         # it will also affect the scheduler output.
@@ -1389,6 +1381,10 @@ class Scheduler(SchedulerInterface):
                     request_id=req_id,
                 )
 
+            # Free encoder inputs only after the step has actually executed.
+            if request.has_encoder_inputs:
+                self._free_encoder_inputs(request)
+
             stopped = False
             new_logprobs = None
             new_token_ids = generated_token_ids