I pay off my two Citi Double Cash card multiple times a month almost every month. I've had the first one for 13 months and the second for 4 months.
I've also made multiple payments on my three AmEx cards in recent months, some of my other Citi cards, my Barclays Aviator card and my USBank Flexperk cards. I made two payments on my Chase IHG card a couple of months this year and I made two payments the last two months on my Chase United card.
I never really worried about it and it hasn't been a problem so far. I've been doing this since I started the GC/MO/CU cycle three years ago.