As long as you don't get it coated with oils, your silicone mold can be repaired fairly easily if something went wrong. The photo above shows a hole where the end of the embossing tool slipped before the mold was set up.
Check for Problems - With your master shape still in the mold, try wiggling the visible ends to see if the master feels tightly fitted in the mold. If it is loose, you may have to add more putty at the loose end.
Fixing Gaps and Holes - If your mold has a hole or is separated from the master at one end (like in the photo above), mix a small amount of putty and press it into any visible gaps, leaving the master in place in the mold. Wait until the putty hardens before you check the rest of the mold.
Fixing Major Gaps If your master is very loose in the mold, you may need to trim the mold and discard the loose section. Gently remove the master from the mold and check the inner shape. Are there obvious cracks, folds, or gaps along the interior? A successful clear bottle will need a mold which is as smooth as possible. Look through the mold to see if you can see light where the mold walls are too thin. You can add extra putty to the outside of the mold to strengthen parts if necessary. If you can see where the mold is obviously misshapen, trim back to a clear part of the mold, insert your master shape, and wrap the section you removed the mold material from with fresh putty. Press the putty tightly to the existing hardened putty, as well as to the master shape, then leave the putty to set. Do not continue to press the putty against the shape as it sets, you risk making gaps in your mold.
See the next step for finishing and filling the holes in the bottom end of the mold if your master shape was held in modelling clay.