While many (make that most) natural cleaning products that can be used around the home are beneficial and with very few side effects, it's important to bear in mind that not everything that nature produces is beneficial. The same goes for things described as "herbal". People still have to use common sense. After all, tobacco and cannabis are natural and herbal, and they do one heck of a lot of damage to people every day.
First of all, the basic tools of natural housekeeping such as salt, baking soda and vinegar are harmless. You can eat them without doing yourself any damage. The same goes for any herbal remedies based on familiar fruits, herbs and vegetables that you use in your daily cooking, such as honey, ginger and garlic. So if you're using these, you are safe. Other natural substances used around the home need to be used with some common sense and not approached with the "if it's natural it can't possibly hurt you" attitude.
These should never be taken internally. Some essential oils should never be used in pregnancy - in fact, most essential oils should not be used during pregnancy, with the exception of the citrus oils, lavender, rose, sandalwood, ylang ylang and a handful of others. According to some practitioners, some essential oils should not be used at all by anyone; this list does include the very useful pennyroyal (the best natural flea repellent but also notorious for triggering miscarriages) but also includes more alarming ones like wormwood and bitter almonds. (Bitter almonds are the main natural source of cyanide and were one of the staples used by poisoners in the Renaissance. Enough said.) Don't be an idiot - follow the instructions on the side of the vial the essential oil came in and don't drink the stuff.
Composts and animal manure do contain bacteria. That's partly the point of using them. The bacteria are all very well in your compost heap, where they do a good job of rotting down vegetable and other organic material and turning it into a source of nutrients for your plants. But they can also make you sick. Cover any open wounds to prevent infection when handling compost and wash your hands well afterwards. Also give your vegetables a bit of a wash before eating them to remove any unpleasantness, and don't use animal manure on vegetables within a week of harvesting the plant, just to be on the safe side. Pregnant women should always wear gloves when gardening and take extreme care because of the risk of toxoplasmosis, which can be contracted from soil where cats have done their business - which means any garden soil.
If you can't positively identify a herb, then don't use it. You don't want to poison yourself. Also, certain herbs and plant extracts should only be administered by a qualified herbalist rather than used for DIY remedies. There have been sad stories involving foxgloves - an extract can be obtained from these plants for heart medication (the name of the drug digitalis is derived from the Latin name of the foxglove) but if you go ahead and make yourself a cup of foxglove tea, you will probably poison yourself. A good rule of thumb is: if you can't find it in a list of ingredients or feed it to a rabbit, don't use it. By all means, use natural house cleaners and use herbal medications. But use them with common sense - naturally.