Consuming blackberry seeds is safe especially when you eat the whole fruit or any of its extracts.  Although, eating blackberry seeds can cause some people to have stomach cramps. Blackberry seeds also contain a natural sugar that can sometimes irritate the gut. This natural sugar is most likely only going to affect those who have problems digesting sorbitol. This could result in symptoms involving feeling bloated, stomach cramps, diarrhea, gas and nausea.