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Pull out method is a very risky method and carries high risk of pregnancy.Delayed periods can be due to various reasons as pregnancy,hormonal imbalance, stress, anxiety,eating disorder, underlying causes as ovarian cysts, fibroids etc.
It is difficult to comment without a physical examination.
Ask her to get a Urine test done for pregnancy determination by fresh morning urine sample.Consider visiting a Gynaecologist for evaluation.
Take care!