Are these new or existing subscriptions?
We use Stripes newer API now for recurring subscriptions to create one-off payments when the initial price is different. To do this we're using their free trial API in combination with one-off API. This appears to be working fine in my tests, but if this is happening for you for older subscriptions it's possible it was an old bug. Please see the below screenshots for what to expect. I've initiated another test subscription to retest this, but it won't clear until tomorrow however it looks fine at Stripe.
CBSubs Invoice
Stripe Initial Payment
Stripe Recurring Subscription
You'll notice initial subscriptions under Stripe > Payments. For subscriptions you'll see them under Customers > Subscriptions in a Trial state with their first recurring payment scheduled. The scheduled recurring payment should be at your recurring rate.