diff --git a/src/systems/clock_inference.jl b/src/systems/clock_inference.jl
index d1358c10b6..1c59d3259b 100644
--- a/src/systems/clock_inference.jl
+++ b/src/systems/clock_inference.jl
@@ -186,10 +186,13 @@ function split_system(ci::ClockInference{S}) where {S}
         end
         tss[id] = ts_i
     end
-    tss[continuous_id], tss[1] = tss[1], tss[continuous_id]
-    inputs[continuous_id], inputs[1] = inputs[1], inputs[continuous_id]
-    id_to_clock[continuous_id], id_to_clock[1] = id_to_clock[1], id_to_clock[continuous_id]
-    continuous_id = 1
+    if continuous_id !== 0
+        tss[continuous_id], tss[end] = tss[end], tss[continuous_id]
+        inputs[continuous_id], inputs[end] = inputs[end], inputs[continuous_id]
+        id_to_clock[continuous_id], id_to_clock[end] = id_to_clock[end],
+        id_to_clock[continuous_id]
+        continuous_id = lastindex(tss)
+    end
     return tss, inputs, continuous_id, id_to_clock
 end
 
@@ -267,7 +270,7 @@ function generate_discrete_affect(
             let_block) |> toexpr
         cont_to_disc_idxs = [parameter_index(osys, sym) for sym in input]
         disc_range = [parameter_index(osys, sym) for sym in unknowns(sys)]
-        save_expr = :($(SciMLBase.save_discretes!)(integrator, $(i - 1)))
+        save_expr = :($(SciMLBase.save_discretes!)(integrator, $i))
         empty_disc = isempty(disc_range)
 
         # @show disc_to_cont_idxs
@@ -290,13 +293,13 @@ function generate_discrete_affect(
             # d2c comes last
             # @show t
             # @show "incoming", p
-            result = c2d_obs(integrator.u, p..., t)
+            result = c2d_obs(u, p..., t)
             for (val, i) in zip(result, $cont_to_disc_idxs)
                 $(_set_parameter_unchecked!)(p, val, i; update_dependent = false)
             end
             $(if !empty_disc
                 quote
-                    disc(disc_unknowns, integrator.u, p..., t)
+                    disc(disc_unknowns, u, p..., t)
                     for (val, i) in zip(disc_unknowns, $disc_range)
                         $(_set_parameter_unchecked!)(p, val, i; update_dependent = false)
                     end
@@ -316,6 +319,7 @@ function generate_discrete_affect(
                 $(SciMLStructures.Discrete()), p)
             repack(discretes)
         end)
+
         push!(affect_funs, affect!)
     end
     if eval_expression
diff --git a/test/clock.jl b/test/clock.jl
index d1e7fdd56d..91f96ce201 100644
--- a/test/clock.jl
+++ b/test/clock.jl
@@ -64,10 +64,11 @@ By inference:
 
 ci, varmap = infer_clocks(sys)
 eqmap = ci.eq_domain
-tss, inputs = ModelingToolkit.split_system(deepcopy(ci))
-sss, = ModelingToolkit._structural_simplify!(deepcopy(tss[1]), (inputs[1], ()))
+tss, inputs, continuous_id = ModelingToolkit.split_system(deepcopy(ci))
+sss, = ModelingToolkit._structural_simplify!(
+    deepcopy(tss[continuous_id]), (inputs[continuous_id], ()))
 @test equations(sss) == [D(x) ~ u - x]
-sss, = ModelingToolkit._structural_simplify!(deepcopy(tss[2]), (inputs[2], ()))
+sss, = ModelingToolkit._structural_simplify!(deepcopy(tss[1]), (inputs[1], ()))
 @test isempty(equations(sss))
 d = Clock(t, dt)
 k = ShiftIndex(d)