So, first of all, welcome to the Quilting Board!!
Secondly, your comment "husband and I took a 4 session class" made me smile - you're lucky that your hubby is also involved in this art!
Thirdly, don't worry about your FMQ (free motion quilting) not looking perfect. It takes awhile to really master this. And to be frank, while I've been quilting on my longarm for about 6 years now, I still don't always feel that I have "mastered" FMQ.
And finally, to your original question about batik holes - I recommend that you check the needle in your machine. While the "universal" needles are usually OK to work with, I find that if I buy the "quilting" or "jeans" needles, I have more success attaining the look I want. And, as others have commented, once you wash the quilt, those needle holes will usually disappear, or if not, they are not really all that noticeable.