your needle needs to be the correct size for the thread you are using- if you are not sure visit the Superior Threads website- they have free charts that tell you what size needle to use with what weight thread- and the types of needles to use with the types of threads. if your needle is dull, a knit needle (round tip-used for knit fabrics) or too large it may cause this problem. there is a good chance when the quilt is finished, quilted & bound and laundered for the first time these *pokies* will disappear. I do generally use a black batting when using black fabric- just makes life easier- but that is not always a good option-depending on the top. but the holes will close up- when your finished quilt is laundered for the first time