The relationship between confirmation and milestones is still unclear in the current implementation. While the confirmation process still depends on the Coordinator, milestones are not necessary the indicator of valid transactions.
(see the attached image *full-credit for @Abmushi)
"Milestone" is a bundle that contains two txs and references the previous milestone and another random tx. Every tx inside a transaction bundle, expect the last index one, references a milestone. If all valid transactions that reference a milestone can get confirmed or only transactions that are (directly/inrectly)referenced by a milestone get confirmed; in other words, if milestones matter so much, I think there is no point of getting referenced by other transactions and the confirmation rate of the current network should be much different: either much better or worse.