What do you mean by swelling of gel? Was the size increased? If yes, then by what percentage. Although, after staining and de-staining, usually gels get shrinked a bit. If possible, can you please give your gel picture? That may help in solving your mystery. 

@ David Farringdon Spencer

I do agree with your points which you have described nicely. Specially the % cross linking issues. But that does not affect the polymerization process. Swelling of gel is really a concern. Purity issues can be one of the possible reason but that too I doubt for its role in swelling of gel. Picture of the gel would help.

@ santosh- I will surely provide you the gel picture. The problem arises after staining. The gel gets expand by 1.5 times atleast. 

@David Farringdon Spencer- Thank you very much for your quality explanation. I think I am having purity issue. I am using Elix water and its pH is around 8. I guess there may be acrylic acid formation that could be affecting the size of the gel and its quality after staining.

@ Gaurav Kumar Singh

Acrylamide will never form acrylic acid in pH 8. However, the purity of chemicals used is a concern. You can mail me your gel at my mail id: [email protected].

Thats strange...The gel actually shrinks on keeping it in the staining solution and then eventually comes back to shape at later stages.....It also do not seem to be a problem of water as mentioned above in the comments i guess. You can try one thing. Prepare the staining solution (Commassie) in acetic acid without water. This would take around 2-3 hours to stain. Leave the gel in destaining solution overnight. Hope it helps. Do update if it works.......all the best..

@ David Farringdon Spencer

Thanks for pointing out the pH issue. Acrylic acid is the deamidation product of acrylamide that copolymerize with acrylamide and bis-acrylamide and affects the ion exchange properties of the gel. It lowers the pH of gel and causes artifacts during sample movement. This formation of the acrylic acid can be regulated by maintaining pH close to 7. At pH 8 although it forms acrylic acid, but its formation rate is slow as compared to pH lower than 7. The % of acrylic acid should be below 0.001% (w/w) for smooth running of the gel.

Just to add to the comments of David Farringdon Spencer

It is also advisable to buy ready-made 30% or 40% stock solutions of acrylamide/bis, rather than preparing these yourself, especially if you are still inexperienced. Acrylamide is a potent neurotoxin and carcinogen that can penetrate even intact skin. You definitely don't want to spread any dust around during weighing. That you handle the stuff only with gloves should go without saying. Polyacrylamide is harmless (actually used to make contact lenses), but the gels contain unreacted acrylamide until thoroughly washed (that is, after staining and destaining). In addition, fingerprints may show on the gel with sensitive staining procedures if you handle your gels with bare hands.

To return to the original problem: Due to their high water content, PAG shrink when placed in staining solution, expand slightly in destaining solution and even more (to +/- original size) when rehydrated. A 12% gel should be quite tough even in water, and almost indestructible (low % gels present more of a handling challenge). If your gels are very soft, most likely their percentage isn't what you think it is. In doi:10.1007/978-1-61779-821-4\_48 I have published a very detailed protocol for SDS-PAGE and staining, maybe that can help you.