The Confederate Battle Flag has 13 stars for 13 states. South Carolina seceded in December 1860, followed by five more states: Mississippi, Florida, Alabama, Georgia, and Louisiana in January, and then Texas on the 1st of February.
These seven states met a few days later in Montgomery, Alabama, and formed the Confederate States of America. Jefferson Davis was elected President on February 9th, almost a month before Lincoln was inaugurated in March.
By the middle of May, four more states had seceded and joined the Confederacy: Virginia, Arkansas, Tennessee, and North Carolina for a total of 11 Confederate States. Four slave states – Delaware, Kentucky, Maryland, and Missouri – remained in the Union.
Missouri and Kentucky proclaimed they were neutral in the war, but that ended in Missouri when Union troops arrested the Missouri State Guard and imprisoned them. The State government went into exile, and a war began between the Missouri State Guard and the Union forces. The state government voted to secede in October, and was admitted to the Confederacy.
It was kind of the opposite in Kentucky. Confederate General Polk advanced into Kentucky one day before Union General Grant moved his army into the state. The Kentucky legislature had promised its citizens it would remain neutral unless it was impossible, and to join the South if necessary. But with neutrality broken, the legislature decided to join with the North because Polk had been the first to enter the state. Many Kentucky citizens were very mad about this, and a new legislature was formed and it declared independence, joining the Confederacy. This made a total of 13 Confederate states.
In short, Missouri and Kentucky were claimed by both North and South, and had representatives in both Congresses.