Thoughts are a part of meditation.
Having lots of thoughts during a meditation session is not an indication of incorrect meditation. In fact, thoughts are one of the symptoms of correct meditation.
Thoughts during meditation are caused by the body purifying itself of accumulated stress (overloads). This process of purification causes the mind to become more active which in turn leads to thoughts as the mind cannot be active without content.
In order to get a picture of what happens to a person’s body during meditation, scientific studies on meditators require them to wear so much invasive instrumentation and apparatus that no meditator being measured scientifically ever has had anything but a thought-filled meditation session.
Imagine wearing an electrocardiogram on your chest, 16 electrodes for EEG on your head, having a catheter inserted into your forearm artery, a gas mask over your nose and mouth, and a rectal thermometer taking your temperature, along with several other devices in place - all at once - and then being asked to meditate in the laboratory while knowing you were being measured.
Yet every scientific study published on the wonderful effects of meditation has asked the meditator to meditate under these or similar conditions. After each study, when interviewed, meditators confirm typically that the session was far more thought-filled than their most thought-filled home sessions. Yet it is these studies that demonstrate repeatedly beneficial physiological changes during meditation.
The lesson from this is that a meditator’s subjective assessment of the benefits of a meditation sitting is not an accurate tool for determining what is the full effect of a particular session.
Scientific studies ask the meditator for ten minutes both before and after the proper meditation-measuring phase of the study simply to sit with eyes closed and not use the mantra - to measure the difference between “sitting merely with eyes closed” versus that phase of the sitting during which the subject is “intending to meditate”.
The distinction between these two phases always is dramatic; the “intending-to-meditate” phase of sitting, however thought-filled, will show invariably powerful physiological changes - mostly those related to release of stress and of deep levels of rest, typically up to five times more restful than sleep.
When the body throws off stress during meditation, this causes the mind to march into thoughts and a feeling of buoyancy instead of diving. The benefits of that phase of a sitting (even if it is the nature of an entire sitting) are mostly deferred benefits; those being detected outside the practice. In other words, you will feel better for having done it, even if during it experiences are not as settled as in other sittings.
So continue to give meditation the priority it deserves in order to receive the wonderful benefits noticed by millions of people around the world.