How to label sound events in noisy .wav files
Automatic detection of birdsong is a well studied problem in machine-learning applied to ecoacoustics/bioacoustics. State of the art methods use Convolutional Neural Networks on spectrograms. In binary classification of bird/no-bird they reach AUC ROC of around 0.90 in noisy and mismatched conditions. The DCASE2018 Bird Audio Detection challenge is a good starting point. Open-source code is available for many of the systems, including the challenge winner. Several of the systems could be adapted to Audio Event Recognition to give time-information of predictions.

Note that to verify your approach is working well, you should always also have a manually labeled test-set.