If the throw-in had been on the endline while the clock was running and you felt the defender was willing to trade a warning just to stop the clock (perhaps they were behind by one point), then you can ignore it, by rule. Yeah - like some 8th grader would figure this out.
However, you had a spot throwin with the clock stopped. You should have given the warning.
I may (notice I said "may") change my mind if it was the second warning and the defender gained no advantage by the slight step on the line. After all, he didn't prevent the inbound pass, but was just reacting to a good fake from B1.
BTW - from the way you worded your post, it sounds like there might have been a 5 second violation.
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Yom HaShoah
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