Tengo un proyecto simple con un guión gráfico que contiene solo unUICollectionViewController, construido con Xcode 7.1.1 para iOS 9.1

class ViewController: UICollectionViewController {

    var values = ["tortile", "jetty", "tisane", "glaucia", "formic", "agile", "eider", "rooter", "nowhence", "hydrus", "outdo", "godsend", "tinkler", "lipscomb", "hamlet", "unbreeched", "fischer", "beastings", "bravely", "bosky", "ridgefield", "sunfast", "karol", "loudmouth", "liam", "zunyite", "kneepad", "ashburn", "lowness", "wencher", "bedwards", "guaira", "afeared", "hermon", "dormered", "uhde", "rusher", "allyou", "potluck", "campshed", "reeda", "bayonne", "preclose", "luncheon", "untombed", "northern", "gjukung", "bratticed", "zeugma", "raker"]

    @IBOutlet weak var flowLayout: UICollectionViewFlowLayout!
    override func viewDidLoad() {
        super.viewDidLoad()        
        flowLayout.estimatedItemSize = CGSize(width: 10, height: 10)
    }

    override func collectionView(collectionView: UICollectionView, numberOfItemsInSection section: Int) -> Int {
        return values.count
    }

    override func collectionView(collectionView: UICollectionView, cellForItemAtIndexPath indexPath: NSIndexPath) -> UICollectionViewCell {
        let cell = collectionView.dequeueReusableCellWithReuseIdentifier("MyCell", forIndexPath: indexPath) as! MyCell
        cell.name = values[indexPath.row]
        return cell
    }

    override func collectionView(collectionView: UICollectionView, didSelectItemAtIndexPath indexPath: NSIndexPath) {
        values.removeAtIndex(indexPath.row)
        collectionView.deleteItemsAtIndexPaths([indexPath])
    }
}

class MyCell: UICollectionViewCell {

    @IBOutlet weak var label: UILabel!

    var name: String? {
        didSet {
            label.text = name
        }
    }
}

Al eliminar las celdas de la vista de colección, todas las celdas restantes se animan a suestimatedItemSize, y luego vuelva al tamaño correcto.

Curiosamente, esto produce advertencias de restricción de diseño automático para cada celda cuando se produce la animación:

2015-12-02 14:30:45.236 CollectionTest[1631:427853] Unable to simultaneously satisfy constraints.
    Probably at least one of the constraints in the following list is one you don't want. 
    Try this: 
        (1) look at each constraint and try to figure out which you don't expect; 
        (2) find the code that added the unwanted constraint or constraints and fix it. 
    (Note: If you're seeing NSAutoresizingMaskLayoutConstraints that you don't understand, refer to the documentation for the UIView property translatesAutoresizingMaskIntoConstraints) 
(
    "<NSAutoresizingMaskLayoutConstraint:0x14556f780 h=--& v=--& H:[UIView:0x1456ac6c0(10)]>",
    "<NSLayoutConstraint:0x1456acfd0 UIView:0x1456ac6c0.trailingMargin == UILabel:0x1456ac830'raker'.trailing>",
    "<NSLayoutConstraint:0x1456ad020 UILabel:0x1456ac830'raker'.leading == UIView:0x1456ac6c0.leadingMargin>"
)

Will attempt to recover by breaking constraint 
<NSLayoutConstraint:0x1456acfd0 UIView:0x1456ac6c0.trailingMargin == UILabel:0x1456ac830'raker'.trailing>

Mi pensamiento inicial fue que romper estas restricciones era lo que estaba causando el problema de cambio de tamaño.

Actualización de la celdaawakeFromNib método:

override func awakeFromNib() {
    super.awakeFromNib()
    contentView.translatesAutoresizingMaskIntoConstraints = false
} 

corrige las advertencias, pero el problema aún ocurre.

Traté de volver a agregar mis propias restricciones entre la celda y sucontentView, pero esto no resolvió el problema:

override func awakeFromNib() {
    super.awakeFromNib()
    contentView.translatesAutoresizingMaskIntoConstraints = false

    for constraint in [
        contentView.leadingAnchor.constraintEqualToAnchor(leadingAnchor),
        contentView.trailingAnchor.constraintEqualToAnchor(trailingAnchor),
        contentView.topAnchor.constraintEqualToAnchor(topAnchor),
        contentView.bottomAnchor.constraintEqualToAnchor(bottomAnchor)]
    {
        constraint.priority = 999
        constraint.active = true
    }
}

Pensamientos?