Cardinality discrepancy
The cardinalities are estimates.
They have limited use, so don't worry if the values are as far off as you see.


If you are worried that some queries are being Optimized inadequately, let's see the queries, SHOW CREATE TABLE, and EXPLAIN SELECT ...  There are many things that can be looked at; most do not involve cardinality.

A typical solution involves a "composite" index.  For example:

WHERE a=1 AND b=2


If you have INDEX(a), INDEX(b), the Optimizer will use only one of the indexes and may use cardinality to decide between them.

If you have INDEX(a,b), the decision is obvious, and cardinality is irrelevant, and the query will run faster.