Pool of objects with objects that are already on the scene in advance

this one helps. Ok, auto answer ;-p
There are fields in the implementations that control exactly that. For example, in the implementation GenericObjectPool, there is the field DEFAULT_MIN_EVICTABLE_IDLE_TIME_MILLIS that says how much time can be an idle object in the pool before being eligible for eviction.

I wish did fix the issue. Consider the Pane#getChildren method. You can loop in the list, and if you find a Pane, you can recursively call the method again.
Be careful because not JavaFX elements are subclass of Pane.

hope this fix your issue minEvictableIdleTimeMillis does not honor the minIdle, what you are looking for is softMinEvictableIdleTimeMillis. Refer to the below documentation :
https://commons.apache.org/proper/commons-pool/apidocs/org/apache/commons/pool2/impl/BaseGenericObjectPool.html#setSoftMinEvictableIdleTimeMillis(long)

I think the issue was by ths following , Your SceneController passes it's transform to the GameMap Setup method. (I assume that the SceneController transform is the "app" object?)
The GameMap Setup method then creates the gates and uses the given parentTransform as a parent for each gate (because it's passend in the GameObject.Instantiate method)

it helps some times Assuming that the destroy / create new approach is OK and you are using version 2.0+ of commons pool, you can use abandoned object tracking and removal to make sure capacity is not permanently leaked when objects are borrowed and never returned. See the javadoc for AbandonedConfig for the configuration settings and the GenericObjectPool constructor that takes an AbandonedConfig instance as an argument. With abandoned object tracking and removal enabled, the pool will destroy instances that have been borrowed but not returned for longer than the removeAbandonedTimeout when the pool is low on capacity.
If for some reason you have to use a version 1.x pool, you can grab the source or use directly the AbandonedObjectPool that ships with DBCP 1.x.