Gentlemen,

I gave up with this error and made override for problematic places:

Code:
Ext.define('MyApp.common.override.DefaultLayout', {
    override: 'Ext.layout.Default',

    removeInnerItem: function(item) {
        if(item && item.element) {
            item.element.detach();
        }
    },

    onItemInnerStateChange: function(item, isInner, destroying) {
        if (isInner) {
            if(this.container && this.container.innerElement) {
                this.insertInnerItem(item, this.container.innerIndexOf(item));
            }
        } else {
            this.removeInnerItem(item);
        }
    }
});
Code:
Ext.define('MyApp.common.override.Component', {
    override: 'Ext.Component',

    toggleCls: function(className, force) {
        if(this.element) {
            this.element.toggleCls(className, force);
            return this;
        }
    }
});
It works in ST 2.3.1.
Hope it helps.