Yes, methane and hydrogen can explode during colonoscopic polyp removal.
Yes, this has really happened.
However, cleaning the colon is not necessarily sufficient to prevent such explosion.
See Fatal colonic explosion during colonoscopic polypectomy, Gastroenterology (1979) vol. 77, pages 1307-10.
The colon appeared very clean and contained
no fecal matter...there was an explosion
which was audible in the endoscopy room, the patient
jerked upwards off the endoscopy table, and the colonoscope
was completely ejected. The patient was immediately transferred to the operating
theater, and laparotomy was carried out 15 min after explosion.
Immediately on opening the abdomen a hemoperitoneum
was visible. There was no fecal matter in the
abdomen. Examination of the colon showed numerous
full-thickness lacerations in the right colon and the transverse
colon as far as the splenic flexure. There were multiple
bleeding points around these perforations. In addition
the spleen was found to have numerous capsular
lacerations. An extended right hemicolectomy was carried
out to include the right colon, the transverse colon, and the
splenic flexure. Massive blood transfusion was continued
during the whole procedure; the patient received 45 units
of blood. Multiple bleeding points occurred in all areas of
dissection (right flank, left hypochondrium, and the pancreatic
region), and it proved impossible to achieve hemostasis.
There was presumably a serious coagulation defect
as a result of the multiple transfusions, and the surgeon
closed the abdomen after packing the abdomen. Death occurred
a few minutes later.