From Lehninger Principles of Biochemistry :
The stability of YAC increases with size (up to a limit). Those with inserts of less than 100000 are gradually lost during mitosis.
Why does this happen ? (YAC refers to yeast artificial chromosome )
This is a question which is not easy to answer, especially the 50.000bp number (which I haven't found anywhere in there literature). However, I found some evidence, partly derived from plant and mammal artificial chromosomes (references 1 and 2), partly from the original publication from Murray and colleagues (reference 3).
The problems with small chromosomes seems to be their passage through mitosis and meiosis, where smaller artificial chromosomes tend to get lost. They are also not controlled very well in their number.
Murray states that YACs of 55kB in size are relatively stable in the yeast cells are relatively stable, but have a lower stability than natural chromosomes. When you are interested in the deeper details, I recommend reading the article.