IP and Missed Base

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In a JUCO game last year, I had a throw to the plate hit R1's foot which caused her to misstep and miss the plate. As the throw caromed away, a subsequent runner (R2) came around to score. The offensive dugout shouted out to R1 to "touch the plate!!" Meanwhile F2 retrieves the ball and headed toward R1 while R1 heads for the plate. F2 is late getting to R1 and as R1 touches the plate, F2 gives up trying to tag her and returns the ball to F1.

DHC comes out and says, "Isn't the second runner out?" I asked why. She said, "Because she passed the first runner when she missed the plate!" I explained that passing a runner only occurs when a runner physically passes a runner and since that did not occur in this situation, there is no out for passing a runner.

Then, the DHC says, "Well, she did miss the plate, didn't she?"

At this point, I'm trying to figure out the best way to handle the situation. I'm asking myself, "Should I treat her question as a valid appeal?" So, instead of doing so, I just say, "Yes, she did." Then, the coach says, "Okay," and heads back to the dugout. She never asked for an appeal and just accepted my explainations. She must have thought that she could legally retouch despite a succeeding runner scoring.

My thought process at the time was: if she didn't feel the other team did something illegal, I wasn't going to point her in that direction moreso than I already had. I had given her all the information she needed to appeal, but she never used that word. However, ever since, I have questioned whether, or not, I handled the situation correctly. Should I have treated her question as an appeal? Was she just asking for information?

What say the board?