Its obvious how two kingdoms can be combined into one through marriage. Was there a corresponding process causing kingdoms to separate that prevented kingdoms from become ever larger and fewer in number?
Kingdoms could become united through marriage and inheiritence.
If Mary, Queen of Scots, had had children from her marriage with the Dauphin of France, the heir (if male, France held with 'Salic inheiritence', meaning that women could not become monarchs) would have been King of France and King of Scotland, and the two countries would have been in a Union of Crowns.
Scotland and England did become a Union of Crowns, when James VI of Scotland became King James I of England. Denmark, Norway and Sweden were in a Union of Crowns (the 'Kalmar Union') in the Middle Ages, and Denmark and Norway remained in a Union of Crowns until 1815 (then Sweden and Norway were in a Union of Crowns).
The marriage of Ferdinand and Isabella united Castille and Aragon and created Spain.
Portugal and Spain were in a Union of Crowns for a while.
This was pretty common in European history.
Actually, it's very rare for two kingdoms to unite through marriage. All medieval kingdoms either forbade women from inheriting the realm at all, or practiced male-preference primogeniture where a woman would inherit only if she had no older or younger brothers.
For example, Mary Queen of Scots took the throne only because her two legitimate brothers died in childhood before their father. (She also had two illegitimate half-brothers, but illegitimate children were hardly ever counted worthy to inherit.) Isabella of Castille had one elder brother and one younger brother; when their father died, the elder brother took the throne with the younger as his heir, and Isabella only came to the throne after they both died.
In addition, women were usually considered unfit to rule at all. King Henry I of England, to guard against this, had his barons all repeatedly swear allegiance to his only daughter Matilda. However, on Henry's death, his nephew Stephen - with support from the Church - immediately rebelled. Even centuries later, Henry VIII would divorce and execute multiple wives to seek a male heir - even though his first wife had given him a daughter Mary, and his second wife had given him Elizabeth. (Both daughters would later reign on their own, however, but there were still protests. "The Queen is a woman!" one Englishwoman would exclaim in shock at seeing Elizabeth in her coronation procession.)
So, there was no need for a countervailing process to separate kingdoms, as they were hardly ever combined by marriage in the first place. It did happen - witness Ferdinand of Aragon and Isabella of Castille, or the later Habsburgs - but it was rare. Even those examples, note, are in the tail end of the Middle Ages or the Early Modern Age.