diff --git a/js/common/model/BunnyCollection.ts b/js/common/model/BunnyCollection.ts
index 7c3fce94..ffa08691 100644
--- a/js/common/model/BunnyCollection.ts
+++ b/js/common/model/BunnyCollection.ts
@@ -30,6 +30,7 @@ import SelectedBunnyProperty from './SelectedBunnyProperty.js';
 import BunnyCounts from './BunnyCounts.js';
 import NaturalSelectionUtils from '../NaturalSelectionUtils.js';
 import isSettingPhetioStateProperty from '../../../../tandem/js/isSettingPhetioStateProperty.js';
+import isClearingPhetioDynamicElementsProperty from '../../../../tandem/js/isClearingPhetioDynamicElementsProperty.js';
 
 const LITTER_SIZE = 4;
 assert && assert( LITTER_SIZE === 4,
@@ -181,17 +182,18 @@ export default class BunnyCollection {
           }
         } );
 
-        this.liveBunnies.push( bunny );
+        // liveBunnies (and all arrays) are stateful, so they will have their own state set separately.
+        !isSettingPhetioStateProperty.value && this.liveBunnies.push( bunny );
       }
       else {
         assert && assert( isSettingPhetioStateProperty.value,
           'a dead bunny should only be created when restoring PhET-iO state' );
-        this.deadBunnies.push( bunny );
       }
     } );
 
     // When a bunny is disposed, remove it from the appropriate arrays. removeListener is not necessary.
     bunnyGroup.elementDisposedEmitter.addListener( bunny => {
+      assert && assert( !( isSettingPhetioStateProperty.value && !isClearingPhetioDynamicElementsProperty.value ), 'should never dispose a bunny while setting state outside of initial clear' );
 
       const liveIndex = this.liveBunnies.indexOf( bunny );
       if ( liveIndex !== -1 ) {
@@ -216,6 +218,12 @@ export default class BunnyCollection {
 
     this.genePool = genePool;
     this.bunnyGroup = bunnyGroup;
+
+    if ( assert && Tandem.PHET_IO_ENABLED ) {
+      phet.phetio.phetioEngine.phetioStateEngine.stateSetEmitter.addListener( () => {
+        this.assertValidCounts();
+      } );
+    }
   }
 
   public dispose(): void {
diff --git a/js/common/model/createBunnyArray.ts b/js/common/model/createBunnyArray.ts
index 6009618e..5e836d40 100644
--- a/js/common/model/createBunnyArray.ts
+++ b/js/common/model/createBunnyArray.ts
@@ -16,6 +16,7 @@ import naturalSelection from '../../naturalSelection.js';
 import Bunny from './Bunny.js';
 import BunnyCounts from './BunnyCounts.js';
 import isSettingPhetioStateProperty from '../../../../tandem/js/isSettingPhetioStateProperty.js';
+import Tandem from '../../../../tandem/js/Tandem.js';
 
 // Additional properties that will be added to ObservableArray<Bunny>
 type AdditionalProperties = {
@@ -39,8 +40,7 @@ export default function createBunnyArray( providedOptions: BunnyArrayOptions ):
     countsPropertyFeatured: false,
 
     // ObservableArrayOptions
-    phetioType: createObservableArray.ObservableArrayIO( ReferenceIO( Bunny.BunnyIO ) ),
-    phetioState: false
+    phetioType: createObservableArray.ObservableArrayIO( ReferenceIO( Bunny.BunnyIO ) )
   }, providedOptions );
 
   // We want to add countsProperty later, so do a little TypeScript hackery here to make that possible.
@@ -50,8 +50,7 @@ export default function createBunnyArray( providedOptions: BunnyArrayOptions ):
     tandem: options.tandem.createTandem( 'countsProperty' ),
     phetioValueType: BunnyCounts.BunnyCountsIO,
     phetioFeatured: options.countsPropertyFeatured,
-    phetioReadOnly: true,
-    phetioState: false // because counts will be restored as Bunny instances are restored to BunnyGroup
+    phetioReadOnly: true
   } );
 
   bunnyArray.countsProperty = countsProperty;
@@ -80,6 +79,13 @@ export default function createBunnyArray( providedOptions: BunnyArrayOptions ):
     }
   } );
 
+  // State may set in an unexpected order, but by the end, we must have the right counts.
+  if ( assert && Tandem.PHET_IO_ENABLED ) {
+    phet.phetio.phetioEngine.phetioStateEngine.stateSetEmitter.addListener( () => {
+      assert && assert( countsProperty.value.totalCount === bunnyArray.length, 'counts out of sync' );
+    } );
+  }
+
   bunnyArray.dispose = () => {
     Disposable.assertNotDisposable();
   };