What negative effects are you talking about? If you mean pre-workout, the only stretching you should do is dynamic stretching, joint mobilisation and activities to increase blood flow and heart rate such as a light jog.
Post-workout, a good strong static stretch is extremely beneficial, it can aid the lymph system in removing toxins built up in the muscle tissue, it will help minimise muscle imbalance and keep muscles at the correct length, which means they will operate better and stronger.
The day after or whenever delayed onset muscle soreness (DOMS) sets in, the best thing you can do to relieve the pain to stay active, jogging, walking etc. This keeps blood circulation up and helps bring in nutrients to repair muscle tissue.